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CP/MM Tutorial
GRS, WS 2010/2011
Emiliano Ippoliti: e.ippoliti@grs-sim.de

We want to study the effect of the solvent (water) and the temperature on the dipole
moment of an acetone molecule. To accomplish that we will resort to several different
software (MOLDEN, CPMD, VMD, Gaussian09, Amber, GROMOS, etc) in order to
let you taste the everyday working in the biophysical field.

The procedure can be summarized in the following steps:

1. Calculate the dipole moment D
v
of acetone in vacuum
2. Perform a QM/MM molecular dynamics simulation for the acetone in a
classical water box at room temperature.
3. Calculate the dipole moment D for some random snapshots of this simulation
and take the mean value
4. Calculate the difference D - D
v


Each file mentioned in this tutorial (in bold) can be found in the folder:

/work/Tutorial/ACETONE/

under the subfolder whose name starts with the number of the corresponding section
of this tutorial.

To do your tests and exercises, work in your own folder that you can create in the
directory:
/work/Tutorial

by the command: mkdir /work/Tutorial/your_name

Then go to your folder: cd /work/Tutorial/your_name

1 - Where to start?

Acetone is the organic compound with the formula (CH3)
2
CO. This colorless, mobile,
flammable liquid is the simplest example of the ketones:


!"#$%& () Acetone

To obtain an initial structure we use the MOLDEN program
1
that can be run simply
typing:

1
http:¡¡www.cmbi.iu.nl¡moluen¡moluen.html
2
source /home/ippoliti/PROGRAMS/modules/molden.sh
molden &

In the Molden Control panel at the right, deselect the “Shade” button and press on the
“ZMAT Editor” button that is a tool to create and/or manipulate structures on screen
and to optimize the structures on a force field level.
The use of the editor is rather intuitive.
2
In the following a synthetic list of the steps to
create the acetone molecule:

• Press “Add line”
• Select Carbon from the Periodic Table
• Press “Substitute atom by Fragment” and without releasing the mouse button
select the –HC=O
• Press “Add line”
• Select Hydrogen from the Periodic Table
• Click, in the Main screen, on the 4 atoms H,C,O,H in sequence to define the
connectivity of the new H atom in the molecule
• Highlight a Hydrogen by pressing on the atom in the Main screen or in the list
of atoms in Zmat Editor
• Press “Substitute atom by Fragment” and without releasing the mouse button
select the –CH3
• Do the same for the other Hydrogen

Then, we can save the structure in the xyz format by writing the name of the file in
the field “File name?”, choosing the “XYZ” format in the menu which appear when
you press on the square “Cartesian” at the right bottom and finally pressing “Write Z-
Matrix”.
Close the ZMAT Editor by clicking the “Close” button on the right top and then by
pressing on the button with a skull.


2 - Dipole moment in vacuum

We will use CPMD to calculate the dipole moment of acetone in gas phase.
To initialize the environment and be able to use CPMD:

source /home/ippoliti/PROGRAMS/modules/cpmd.sh

Each node of the cluster (one node has been assigned to each terminal in the
classroom) has 8 cores. To run CPMD with all the cores (single line):

mpirun –np 8 cpmd.x input_file
/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > output_file &


2
An online geneial guiue foi the ZNAT Euitoi can be founu at the web auuiess:
http:¡¡www.cmbi.iu.nl¡moluen¡zmat¡zmat.html#auu

S
/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP is the location where CPMD will
look for the pseudopotentials files which will be specified in the input file. All the
pseudopotentials we will use are already present there.

In order to calculate the dipole moment of the acetone in vacuum we first have to
optimize the geometry of the molecule we have constructed in the previous step. So,
we need to write an appropriate input file according the syntax of CPMD.
3
By your
favorite editor, write down the opt_geo.inp text file:

&INFO
Acetone molecule
Geometry optimization
&END

&CPMD
OPTIMIZE GEOMETRY XYZ
CONVERGENCE ORBITALS
1.0d-7
CONVERGENCE GEOMETRY
7.0d-4
&END

&SYSTEM
ANGSTROM
SYMMETRY
ORTHORHOMBIC
CELL ABSOLUTE
10.6 10.0 9.8 0.0 0.0 0.0
CUTOFF
70.
&END

&DFT
FUNCTIONAL BLYP
&END

&ATOMS
*C_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=D
3
0.000000 0.000000 0.000000
1.367073 0.000000 -0.483333
-0.683537 -1.183920 -0.483333

*O_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=D
1
0.000000 0.000000 1.220000

*H_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=P
6
1.367073 0.000000 -1.572333
1.880433 0.889165 -0.120333
1.880433 -0.889165 -0.120333
-0.683537 -1.183920 -1.572333
-0.170177 -2.073085 -0.120333
-1.710256 -1.183920 -0.120333
&END



S
CPNB manual: http:¡¡www.cpmu.oig¡manual.puf
4
CPMD Input file

Any CPMD input file is organized in sections that start with &NAME and end with
&END. Everything outside those sections is ignored. Also all keywords have to be in
upper case or else they will be ignored. The sequence of the sections does not matter,
nor does the order of keywords (except in some special case reported in the manual).
A minimal input file must have a &CPMD, &SYSTEM, and an &ATOMS section.

This input file starts with an (optional) &INFO section. This section allows you to put
comments about the calculation into the input file and they will be repeated in the
output file. This can be very useful to identify and match your input and output files.

The first part of &CPMD section instructs the program to do a geometry optimization
(XYZ suboption specify you want the final structure also in xyz format in a file called
GEOMETRY.xyz and a ’trajectory’ of the optimization in a file named
GEO_OPT.xyz) with a tight wavefunction and geometry convergence criterions
respectively (default 10
-5
and 5*10
-4
).

The &SYSTEM section contains various parameters related to the simulation cell and
the representation of the electronic structure. The keywords SYMMETRY, CELL and
CUTOFF are required and define the (periodic) symmetry, shape, and size of the
simulation cell, as well as the plane wave energy cutoff (i.e. the size of the basis set),
respectively. The keyword ANGSTROM specify that the atomic coordinates and the
supercell parameters and several other parameters are read in Ångstroms
(pay attention: default is atomic units (a.u.) which are always used internally). We
define a primitive orthorhombic cell with the lattice constants obtained by adding 7 Å
in each direction to the dimension of the system: the cell has to be large enough to
avoid significant interactions of the acetone molecule and its electron structure with
its periodic neighbors. In CPMD all calculations are periodic. Do always a
convergence test looking for example at the total energy value when you increase the
box size!

The &DFT section is used to select the density functional (FUNCTIONAL) and
related parameters. In this case we use the gradient corrected BLYP functional
4
(local
density approximation is the default).

Finally, the &ATOMS section is needed to specify the atom coordinates and the
pseudopotential(s), that are used to represent them. The coordinates are taken from
the structure written by MOLDEN.
The input for a new atom type is started with a ``*'' in the first column. This line
further contains the file name where to find the pseudopotential information starting
in column 2 and several labels as KLEINMAN-BYLANDER, in our case, which
specifies the method to be used for the calculation of the nonlocal parts of the
pseudopotential (this method is extremely efficient but also accurate).
The next line contains information on the nonlocality of the pseudopotential: you can
specify the maximum l-quantum number with ``LMAX= l '' where l is S, P or D.
5


4
A.B. Becke, }.Chem.Phys. 98 (199S) S648-S6S2; C. Lee, W. Yang, R.u. Paii, Phys. Rev. B S7
(1988) 78S-789.
S
On the following lines the coordinates for this atomic species have to be given.
The first line gives the number of atoms of the current type.
---

If you start the geometry optimization (single line):

mpirun -np 8 cpmd.x opt_geo.inp
/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > opt_geo.out &

the calculation should be completed in less than a minute 5 minutes (use
tail –f opt_geo.out
to monitor the different steps of the calculation reported in the output file).

CPMD Output file

Look at the output file to understand all the information which we can find there.
At the beginning there is the header where one can see, when the run was started,
what version of CPMD was used, and when it was compiled:

PROGRAM CPMD STARTED AT: Tue Jun 1 19:32:59 2010

SETCNST| USING: CODATA 2006 UNITS


****** ****** **** **** ******
******* ******* ********** *******
*** ** *** ** **** ** ** ***
** ** *** ** ** ** ** **
** ******* ** ** ** **
*** ****** ** ** ** ***
******* ** ** ** *******
****** ** ** ** ******

VERSION 3.13.2


COMPILED WITH GROMOS-AMBER QM/MM SUPPORT

COPYRIGHT
IBM RESEARCH DIVISION
MPI FESTKOERPERFORSCHUNG STUTTGART

The CPMD consortium
Home Page: http://www.cpmd.org
Mailing List: cpmd-list@cpmd.org
E-mail: cpmd@cpmd.org


*** Jan 12 2010 -- 16:03:39 ***


Then, we find some technical information about the environment (machine, user,
directory, input file, process id) where this job was run:

THE INPUT FILE IS: opt_geo.inp
THIS JOB RUNS ON: iff105c19
THE CURRENT DIRECTORY IS:
/local/GRS/Users/Tutorials/ACETONE/2-CPMD
THE TEMPORARY DIRECTORY IS:
/local/GRS/Users/Tutorials/ACETONE/2-CPMD

S
If this is the only input, the program assumes that LMAX is the l for the local
potential. You can use another local function by specifying ``LOC= ''. In addition it is
possible to assign the local potential to a further potential with ``SKIP= ''.
6
THE PROCESS ID IS: 28735

Next are the contents of the &INFO section copied to the output:



******************************************************************************
* INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO - INFO *
******************************************************************************
* Acetone molecule *
* Geometry optimization *
******************************************************************************


Next section contain a summary of some of the parameters read in from the &CPMD
section, or their respective default settings; for example the convergence threshold for
wavefunction optimization (set manually) or the maximum number of iterations
(default):

OPTIMIZATION OF IONIC POSITIONS

PATH TO THE RESTART FILES: ./
GRAM-SCHMIDT ORTHOGONALIZATION
MAXIMUM NUMBER OF STEPS: 10000 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING EXTENDED BULK BEHAVIOR
FICTITIOUS ELECTRON MASS: 400.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
CONVERGENCE CRITERIA FOR WAVEFUNCTION OPTIMIZATION: 1.0000E-06
WAVEFUNCTION OPTIMIZATION BY PRECONDITIONED DIIS
THRESHOLD FOR THE WF-HESSIAN IS 0.5000
MAXIMUM NUMBER OF VECTORS RETAINED FOR DIIS: 10
STEPS UNTIL DIIS RESET ON POOR PROGRESS: 10
FULL ELECTRONIC GRADIENT IS USED
CONVERGENCE CRITERIA FOR GEOMETRY OPTIMIZATION: 3.000000E-04
GEOMETRY OPTIMIZATION BY GDIIS/BFGS
SIZE OF GDIIS MATRIX: 5
GEOMETRY OPTIMIZATION IS SAVED ON FILE GEO_OPT.xyz
EMPIRICAL INITIAL HESSIAN (DISCO PARAMETRISATION)
SPLINE INTERPOLATION IN G-SPACE FOR PSEUDOPOTENTIAL FUNCTIONS
NUMBER OF SPLINE POINTS: 5000


The exchange correlation functionals are reported in the lines coming immediately
after:

EXCHANGE CORRELATION FUNCTIONALS
LDA EXCHANGE: SLATER (ALPHA = 0.66667)
LDA CORRELATION: LEE, YANG & PARR
[C.L. LEE, W. YANG, AND R.G. PARR, PRB 37 785 (1988)]
GRADIENT CORRECTED FUNCTIONAL
DENSITY THRESHOLD: 1.00000E-08
EXCHANGE ENERGY
[A.D. BECKE, PHYS. REV. A 38, 3098 (1988)]
PARAMETER BETA: 0.004200
CORRELATION ENERGY
[LYP: C.L. LEE ET AL. PHYS. REV. B 37, 785 (1988)]

At this point of the output you find which and how many atoms (and their coordinates
in a.u.), electrons and states (we are doing a closed shell calculation, so there are only
doubly occupied states) are in the system, and what pseudopotentials were used with
which settings:
7

*** DETSP| SIZE OF THE PROGRAM IS 3700/ 119392 kBYTES ***

***************************** ATOMS ****************************
NR TYPE X(bohr) Y(bohr) Z(bohr) MBL
1 C 0.000000 0.000000 0.000000 3
2 C 2.583394 0.000000 -0.913367 3
3 C -1.291698 -2.237285 -0.913367 3
4 O 0.000000 0.000000 2.305466 3
5 H 2.583394 0.000000 -2.971279 3
6 H 3.553503 1.680278 -0.227396 3
7 H 3.553503 -1.680278 -0.227396 3
8 H -1.291698 -2.237285 -2.971279 3
9 H -0.321588 -3.917563 -0.227396 3
10 H -3.231915 -2.237285 -0.227396 3
****************************************************************

NUMBER OF STATES: 12
NUMBER OF ELECTRONS: 24.00000
CHARGE: 0.00000
ELECTRON TEMPERATURE(KELVIN): 0.00000
OCCUPATION
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0

============================================================
| Pseudopotential Report Tue Jan 14 09:55:25 1997 |
------------------------------------------------------------
| Atomic Symbol : C |
| Atomic Number : 6 |
| Number of core states : 1 |
| Number of valence states : 2 |
| Exchange-Correlation Functional : |
| Slater exchange : .6667 |
| LDA correlation : Lee-Yang-Parr |
| Exchange GC : Becke (1988) |
| Correlation GC : Lee-Yang-Parr |
| Electron Configuration : N L Occupation |
| 1 S 2.0000 |
| 2 S 2.0000 |
| 2 P 2.0000 |
| Full Potential Total Energy -37.702121 |
| Trouiller-Martins normconserving PP |
| n l rc energy |
| 2 S 1.2300 -.49630 |
| 2 P 1.2300 -.19186 |
| 3 D .7159 -.19186 |
| Number of Mesh Points : 615 |
| Pseudoatom Total Energy -5.370516 |
============================================================

============================================================
| Pseudopotential Report Thu Nov 30 13:19:26 1995 |
------------------------------------------------------------
| Atomic Symbol : O |
| Atomic Number : 8 |
| Number of core states : 1 |
| Number of valence states : 2 |
| Exchange-Correlation Functional : |
| Slater exchange : .6667 |
| LDA correlation : Lee-Yang-Parr |
| Exchange GC : Becke (1988) |
| Correlation GC : Lee-Yang-Parr |
| Electron Configuration : N L Occupation |
| 1 S 2.0000 |
| 2 S 2.0000 |
| 2 P 4.0000 |
| Full Potential Total Energy -75.023693 |
| Trouiller-Martins normconserving PP |
| n l rc energy |
| 2 S 1.0500 -.87404 |
| 2 P 1.0500 -.33186 |
| 3 D 1.0500 -.33186 |
| Number of Mesh Points : 631 |
| Pseudoatom Total Energy -15.775323 |
============================================================

============================================================
| Pseudopotential Report Thu Nov 30 13:17:19 1995 |
8
------------------------------------------------------------
| Atomic Symbol : H |
| Atomic Number : 1 |
| Number of core states : 0 |
| Number of valence states : 1 |
| Exchange-Correlation Functional : |
| Slater exchange : .6667 |
| LDA correlation : Lee-Yang-Parr |
| Exchange GC : Becke (1988) |
| Correlation GC : Lee-Yang-Parr |
| Electron Configuration : N L Occupation |
| 1 S 1.0000 |
| Full Potential Total Energy -.462611 |
| Trouiller-Martins normconserving PP |
| n l rc energy |
| 1 S .5000 -.24002 |
| 2 P .5000 -.24002 |
| Number of Mesh Points : 511 |
| Pseudoatom Total Energy -.462591 |
============================================================

****************************************************************
* ATOM MASS RAGGIO NLCC PSEUDOPOTENTIAL *
* C 12.0112 1.2000 NO KLEINMAN S NONLOCAL *
* P NONLOCAL *
* D LOCAL *
* O 15.9994 1.2000 NO KLEINMAN S NONLOCAL *
* P NONLOCAL *
* D LOCAL *
* H 1.0080 1.2000 NO KLEINMAN S NONLOCAL *
* P LOCAL *
****************************************************************


Then, a section about how the calculation is distributed through the 8 cores: here you
can understand if something wrong happened and you run for example only a serial
job:

PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA
NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES
0 4333 34682 13 246 976 1 1
1 4335 34684 14 246 976 2 1
2 4336 34639 13 243 975 1 1
3 4336 34676 14 244 976 2 1
4 4334 34682 13 244 976 1 1
5 4332 34670 14 244 976 2 1
6 4338 34676 13 244 976 1 1
7 4342 34680 14 244 976 2 1
G=0 COMPONENT ON PROCESSOR : 2
PARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARAPARA

*** LOADPA| SIZE OF THE PROGRAM IS 10260/ 120760 kBYTES ***

OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN
NUMBER OF CPUS PER TASK 1
OPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPENMPOPEN

*** RGGEN| SIZE OF THE PROGRAM IS 11492/ 121976 kBYTES ***

The following part of the output we see a summary of the settings read in from the
&SYSTEM section of the input file or their corresponding defaults and some derived
parameters (density cutoff, number of plane waves):

************************** SUPERCELL ***************************
SYMMETRY: ORTHORHOMBIC
LATTICE CONSTANT(a.u.): 20.03110
CELL DIMENSION: 20.0311 0.9434 0.9245 0.0000 0.0000 0.0000
VOLUME(OMEGA IN BOHR^3): 7010.16987
LATTICE VECTOR A1(BOHR): 20.0311 0.0000 0.0000
LATTICE VECTOR A2(BOHR): 0.0000 18.8973 0.0000
LATTICE VECTOR A3(BOHR): 0.0000 0.0000 18.5193
RECIP. LAT. VEC. B1(2Pi/BOHR): 0.0499 0.0000 0.0000
9
RECIP. LAT. VEC. B2(2Pi/BOHR): 0.0000 0.0529 0.0000
RECIP. LAT. VEC. B3(2Pi/BOHR): 0.0000 0.0000 0.0540
REAL SPACE MESH: 108 108 100
WAVEFUNCTION CUTOFF(RYDBERG): 70.00000
DENSITY CUTOFF(RYDBERG): (DUAL= 4.00) 280.00000
NUMBER OF PLANE WAVES FOR WAVEFUNCTION CUTOFF: 34686
NUMBER OF PLANE WAVES FOR DENSITY CUTOFF: 277389
****************************************************************

Here we see how CPMD generates the initial guess for the wavefunction
optimization. In this case it uses a superposition of atomic wavefunctions using an
(internal) minimal Slater basis:

*** RINFORCE| SIZE OF THE PROGRAM IS 16052/ 127264 kBYTES ***
*** FFTPRP| SIZE OF THE PROGRAM IS 19764/ 128656 kBYTES ***

GENERATE ATOMIC BASIS SET
C SLATER ORBITALS
2S ALPHA= 1.6083 OCCUPATION= 2.00
2P ALPHA= 1.5679 OCCUPATION= 2.00
O SLATER ORBITALS
2S ALPHA= 2.2458 OCCUPATION= 2.00
2P ALPHA= 2.2266 OCCUPATION= 4.00
H SLATER ORBITALS
1S ALPHA= 1.0000 OCCUPATION= 1.00


INITIALIZATION TIME: 0.39 SECONDS

*** GMOPTS| SIZE OF THE PROGRAM IS 24656/ 141780 kBYTES ***
*** PHFAC| SIZE OF THE PROGRAM IS 24764/ 152468 kBYTES ***
*** ATOMWF| SIZE OF THE PROGRAM IS 25784/ 154300 kBYTES ***
ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000

****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 C 0.000000 0.000000 0.000000
2 C 2.583394 0.000000 -0.913367
3 C -1.291698 -2.237285 -0.913367
4 O 0.000000 0.000000 2.305466
5 H 2.583394 0.000000 -2.971279
6 H 3.553503 1.680278 -0.227396
7 H 3.553503 -1.680278 -0.227396
8 H -1.291698 -2.237285 -2.971279
9 H -0.321588 -3.917563 -0.227396
10 H -3.231915 -2.237285 -0.227396
****************************************************************


From the following statement in the output you can see that the Hessian has been
initialized from a simple guess assuming a molecule with some specified bonds. This
behavior can be controlled with the keyword HESSIAN. For bulk systems or
complicated molecules, it may be better to start from a unit Hessian instead:


INITIALIZE EMPIRICAL HESSIAN
<<<<< ASSUMED BONDS >>>>>
2 <--> 1 3 <--> 1 4 <--> 1 5 <--> 2 6 <--> 2
7 <--> 2 8 <--> 3 9 <--> 3 10 <--> 3
<<<<< HYDROGEN BONDS >>>>>
5 <--> 1 5 <--> 3 6 <--> 1 6 <--> 4 7 <--> 1
7 <--> 3 7 <--> 4 8 <--> 1 8 <--> 2 9 <--> 1
9 <--> 2 9 <--> 4 10 <--> 1 10 <--> 4
TOTAL NUMBER OF MOLECULAR STRUCTURES: 1

****************************************************************
* ATOMIC COORDINATES *
****************************************************************
1 C 0.000000 0.000000 0.000000
2 C 2.583394 0.000000 -0.913367
3 C -1.291698 -2.237285 -0.913367
4 O 0.000000 0.000000 2.305466
5 H 2.583394 0.000000 -2.971279
1u
6 H 3.553503 1.680278 -0.227396
7 H 3.553503 -1.680278 -0.227396
8 H -1.291698 -2.237285 -2.971279
9 H -0.321588 -3.917563 -0.227396
10 H -3.231915 -2.237285 -0.227396
****************************************************************

Now the program is ready to start the geometry optimization. You can follow the
progress of the optimization in the output file:


CPU TIME FOR INITIALIZATION 0.81 SECONDS


================================================================
= GEOMETRY OPTIMIZATION =
================================================================
NFI GEMAX CNORM ETOT DETOT TCPU
EWALD| SUM IN REAL SPACE OVER 1* 1* 1 CELLS
1 3.015E-02 4.345E-03 -35.648938 -3.565E+01 0.51
2 1.889E-02 1.442E-03 -36.307687 -6.587E-01 0.46
3 1.904E-02 7.725E-04 -36.379166 -7.148E-02 0.46


26 1.294E-06 1.055E-07 -36.415776 -2.343E-09 0.48
27 9.933E-07 7.580E-08 -36.415776 -1.233E-09 0.48

RESTART INFORMATION WRITTEN ON FILE ./RESTART.1

ATOM COORDINATES GRADIENTS (-FORCES)
1 C 0.0000 0.0000 0.0000 -4.443E-02 7.697E-02 -5.004E-02
2 C 2.5834 0.0000 -0.9134 -3.769E-02 -4.835E-02 4.876E-02
3 C -1.2917 -2.2373 -0.9134 6.088E-02 8.661E-03 4.903E-02
4 O 0.0000 0.0000 2.3055 3.158E-02 -5.469E-02 -6.270E-02
5 H 2.5834 0.0000 -2.9713 -1.090E-02 -5.915E-05 8.858E-03
6 H 3.5535 1.6803 -0.2274 -9.255E-03 -3.027E-03 -2.712E-04
7 H 3.5535 -1.6803 -0.2274 6.917E-04 3.287E-03 -1.830E-03
8 H -1.2917 -2.2373 -2.9713 5.515E-03 9.402E-03 8.862E-03
9 H -0.3216 -3.9176 -0.2274 -3.189E-03 1.061E-03 -1.824E-03
10 H -3.2319 -2.2373 -0.2274 7.229E-03 6.496E-03 -2.472E-04
FILE GEO_OPT.xyz EXISTS, NEW DATA WILL BE APPENDED
****************************************************************
*** TOTAL STEP NR. 27 GEOMETRY STEP NR. 1 ***
*** GNMAX= 7.696852E-02 ETOT= -36.415776 ***
*** GNORM= 3.227866E-02 DETOT= 0.000E+00 ***
*** CNSTR= 0.000000E+00 TCPU= 12.89 ***
****************************************************************
1 2.130E-02 5.311E-03 -35.580799 8.350E-01 0.46
2 1.574E-02 1.566E-03 -36.324351 -7.436E-01 0.46
3 5.503E-03 8.729E-04 -36.400043 -7.569E-02 0.46

...


A geometry optimization is not much else than repeated wavefunction optimizations,
where the positions of the atoms are updated according to the forces acting on them.
In the first part above you can see, the wavefunction optimization. The columns have
the following meaning:
• NFI step number (number of finite iterations)
• GEMAX largest off-diagonal component
• CNORM average of the off-diagonal components
• ETOT total energy DETOT change in total energy
• TCPU time used for this step
One can see that the calculation stops after the convergence criterion of 1.0d-6 has
been reached for the GEMAX value.
After printing the positions and forces of the atoms you see a small report block and
then another wavefunction optimization starts. The numbers for GNMAX, GNORM,
11
and CNSTR stand for the largest absolute component of the force on any atom,
average force on the atoms, and the largest absolute component of a constraint force
on the atoms respectively. They allow you to monitor the progress of the convergence
of the geometry optimization.


Finally, at the end of the geometry optimization, you can see that the forces and the
total energy have decreased from their initial values as it is to be expected:

****************************************************************
*** TOTAL STEP NR. 3737 GEOMETRY STEP NR. 214 ***
*** GNMAX= 2.827646E-04 [3.64E-02] ETOT= -36.489908 ***
*** GNORM= 1.395703E-04 DETOT= -1.769E-05 ***
*** CNSTR= 0.000000E+00 TCPU= 9.63 ***
****************************************************************
================================================================
= END OF GEOMETRY OPTIMIZATION =
================================================================

and we have the final summary of the results; the atom coordinates and a breakdown
of the total energy into the various components:

RESTART INFORMATION WRITTEN ON FILE ./RESTART.1

****************************************************************
* *
* FINAL RESULTS *
* *
****************************************************************

ATOM COORDINATES GRADIENTS (-FORCES)
1 C 0.3033 -0.3710 0.4996 2.238E-04 -3.750E-05 -1.867E-04
2 C 2.8157 0.1207 -0.8206 -2.828E-04 1.186E-04 1.534E-04
3 C -1.4005 -2.3884 -0.6592 -1.866E-05 -5.129E-05 1.748E-04
4 O -0.3055 0.7755 2.4178 1.488E-05 -9.553E-05 2.593E-04
5 H 2.5171 0.5750 -2.8280 7.045E-06 -1.029E-04 -2.289E-04
6 H 3.8187 1.6721 0.1124 -6.949E-05 1.507E-04 -3.226E-05
7 H 3.9948 -1.5943 -0.7676 1.188E-04 -1.722E-05 1.350E-04
8 H -1.5584 -2.1576 -2.7186 1.045E-05 -8.026E-05 -1.718E-04
9 H -0.5710 -4.2692 -0.3267 -5.208E-05 -4.544E-05 5.413E-05
10 H -3.2775 -2.3193 0.2103 -1.609E-04 1.615E-04 -2.245E-04

****************************************************************


ELECTRONIC GRADIENT:
MAX. COMPONENT = 8.03517E-07 NORM = 6.81662E-08
NUCLEAR GRADIENT:
MAX. COMPONENT = 2.82765E-04 NORM = 1.39570E-04


TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 24.000000
IN R-SPACE = 24.000000

(K+E1+L+N+X) TOTAL ENERGY = -36.48990756 A.U.
(K) KINETIC ENERGY = 27.70023623 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -27.60801450 A.U.
(S) ESELF = 29.92067103 A.U.
(R) ESR = 1.71581582 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -27.66180959 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 1.82151808 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -10.74183777 A.U.
GRADIENT CORRECTION ENERGY = -0.58344734 A.U.

****************************************************************

The last section of the output reports the memory allocation and the timing of the run:

================================================================
12
BIG MEMORY ALLOCATIONS
SCR 785159 CATOM 190652
PME 520040 PSI 330270
YF 330270 GNL 240960
ATWFR 301200 SCR 785149
XF 330270 RHOE 165135
----------------------------------------------------------------
[PEAK NUMBER 99] PEAK MEMORY 4872541 = 39.0 MBytes
================================================================


****************************************************************
* *
* TIMING *
* *
****************************************************************
SUBROUTINE CALLS CPU TIME ELAPSED TIME
INVFFTN 44858 3172.00 323.62
FFT-G/S 269168 2733.40 274.36
FWFFT 18690 1730.00 175.40
I NVFFT 14953 1726.20 173.92
GCENER 3738 1265.70 128.33
FWFFTN 22436 1242.70 125.49
FFTCOM 33643 817.30 127.30
VPSI 3747 593.00 58.45
GRADEN 3738 460.30 47.00
RHOOFR 3737 448.90 45.11
N-FFTCOM 67294 389.10 84.91
ODIIS 3737 381.20 38.66
XCENER 3738 353.30 35.86
FNONLOC 3747 233.70 23.72
PHASE 33643 219.10 22.22
VOFRHOA 3738 172.50 17.50
VOFRHOB 3738 131.30 12.75
EICALC 3738 94.90 9.90
RNLSM1 3747 66.90 6.84
RGS 3950 38.60 3.57
RNLSM2 664 35.50 3.48
----------------------------------------------------------------
TOTAL TIME 16305.60 1738.41
****************************************************************

CPU TIME : 4 HOURS 33 MINUTES 47.00 SECONDS
ELAPSED TIME : 0 HOURS 30 MINUTES 10.50 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS 41068/ 152348 kBYTES ***

PROGRAM CPMD ENDED AT: Tue Jun 1 20:03:09 2010


================================================================
= COMMUNICATION TASK AVERAGE MESSAGE LENGTH NUMBER OF CALLS =
= SEND/RECEIVE 43407. BYTES 36127. =
= BROADCAST 321. BYTES 15557. =
= GLOBAL SUMMATION 360. BYTES 79725. =
= GLOBAL MULTIPLICATION 0. BYTES 1. =
= ALL TO ALL COMM 876851. BYTES 100937. =
= PERFORMANCE TOTAL TIME =
= SEND/RECEIVE 5675.900 MB/S 0.276 SEC =
= BROADCAST 94.488 MB/S 0.053 SEC =
= GLOBAL SUMMATION 8.258 MB/S 10.435 SEC =
= GLOBAL MULTIPLICATION 0.000 MB/S 0.001 SEC =
= ALL TO ALL COMM 417.428 MB/S 212.029 SEC =
= SYNCHRONISATION 0.025 SEC =
================================================================

If you look in your directory, you will see the following files:

Name Content

GEOMETRY Final ionic positions and velocities (in a.u.)
GEOMETRY.xyz Final ionic positions and velocities in xyz format
GEO_OPT.xyz All the ionic positions along the geometry optimization
HESSIAN Approximate Hessian used in geometry optimization
1S
LATEST Info on the last restart file: filename and # times written
RESTART.1 Restart binary file from which it is possible restart a new
calculation

Now we want to calculate the dipole of the acetone in the “zero temperature”
optimized structure just found by using the RESTART.1 file to retrieve the
information. We can do that modifying the input file this way (see dipole.inp file):

&CPMD
PROPERTIES
RESTART WAVEFUNCTION COORDINATES LATEST
&END

&PROP
DIPOLE MOMENT
&END



PROPERTIES keyword tells CPMD to look at the section &PROP where it is
specifies which properties it has to calculate.

RESTART keyword tells CPMD to read WAVEFUNCTION AND COORDINATES
from the restart file written in the LATEST file (which was generated in the previous
calculation).

The rest of the input file is the same of the previous one: the coordinates will be not
read (since are taken from the restart file) but some number as to put anyway to avoid
the program stops writing some error!

Run the job (single line):

mpirun -np 8 cpmd.x dipole.inp
/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > dipole.out &

In the output file you can see that the following new section:

CALCULATE DIPOLE MOMENT


****************************************************************
* PROPERTY CALCULATIONS *
****************************************************************

RV30| WARNING! NO WAVEFUNCTION VELOCITIES

RESTART INFORMATION READ ON FILE ./RESTART.1
*** PHFAC| SIZE OF THE PROGRAM IS 26772/ 142336 kBYTES ***

CENTER OF INTEGRATION (CORE CHARGE): 0.37726 -0.65932 0.02482

DIPOLE MOMENT
X Y Z TOTAL
0.35426 -0.61017 -0.98996 1.21566 atomic units
0.90044 -1.55090 -2.51623 3.08990 Debye




14
3 – The electrostatic grid

The next will be to create a box with an acetone molecule and several water
molecules. We will use for that the xleap program belonging to the Amber10
6

molecular dynamics package. This package has been devised to deal with biological
systems (aminoacids, nucleic acids, etc) and so our acetone has not recognized by it.
This is also the case when we want to study some drug which interacts with
“traditional” biological systems.
In particular, xleap do not know how to assign the partial charges to each atom of
acetone. To do that we will use a standard procedure which has been directly
suggested by the developers of the Amber force fields and which they use to tune that
parameters which is not possible to determine experimentally. The procedure is based
on calculating at quantum level the electrostatic potential on a grid around the
molecule and then to determine the so-called RESP charges to assign at each atom in
order to reproduce the electrostatic field.
According the recipe of Amber developers we will use the Gaussian09 package
7
to
calculate the electrostatic grid by using the 6-31G(d,p) localized basis set and B3LYP
exchange correlation functional.
First, we need to optimize the geometry again: the level of theory are different and in
principle the optimized structures could be different! Here it is the input file
opt_geom.com for Gaussian:

%NProcShared=8
%chk=./opt_geom.chk
%mem=600MB
#p opt b3lyp/6-31G(d,p) nosymm iop(6/7=3) gfinput

Acetone geometry optimization

0 1
C 0.000000 0.000000 0.000000
O 0.000000 0.000000 1.220000
C 1.367073 0.000000 -0.483333
C -0.683537 -1.183920 -0.483333
H 1.367073 0.000000 -1.572333
H 1.880433 0.889165 -0.120333
H 1.880433 -0.889165 -0.120333
H -0.683537 -1.183920 -1.572333
H -0.170177 -2.073085 -0.120333
H -1.710256 -1.183920 -0.120333

Note: Remember to leave to blank line at the end of the file.

Run the optimization:

1. Initialize the environment:

source /home/ippoliti/PROGRAMS/modules/gaussian.sh

2. Run Gaussian:

g09 opt_geom.com &> /dev/null &


6
You can finu the manual at the web auuiess: http:¡¡ambeimu.oig¡uoc1u¡
7
uaussianu9 online manual: http:¡¡www.gaussian.com¡g_tech¡g_ui¡gu9help.htm
1S
3. After about one minute the job will end and you can check that the
optimization has been successfully this way:

grep -A 1 Maximum opt_geom.log

Use Molden to retrieve the coordinates of the last optimized configuration:

molden opt_geom.log &

in the Molden Control panel press the “Geom. conv.” button and the Geom
Convergence windows will appear. In that window you can select any step of the
optimization procedure; to save the optimized geometry, select the last one and
“write” (save) the structure (in xyz format).

Now, use Gaussian again to calculate the electrostatic grid by the
electrostatic_grid.com input file:
First, make a copy of the checkpoint file from the optimization run:
cp opt_geom.chk electrostatic_grid.chk

%NProcShared=8
%chk=./electrostatic_grid.chk
%mem=600MB
#p b3lyp/6-31G(d,p) nosymm iop(6/33=2) pop(chelpg,regular) guess=read gfinput geom.=check

Acetone electrostatic grid calculation

0 1

(put a blank line at the end)

The wave function (guess=read) as well as the final (“optimized”) coordinates
(geom=check) are read from the checkpoint file. The electrostatic grid will be written in
the log file: look for the string “ESP fit Center”.


4 – Partial charges

The program Antechamber inside the Amber10 package is able to read the electrostatic
grid in a log file of Gaussian and calculate the RESP charges associated to the atoms of
your molecule. To use Antechamber and every other program of the Amber10 suite, we
firstly need to initialize the environment:

source /home/ippoliti/PROGRAMS/modules/amber.sh

Copy the log file of Gaussian with the electrostatic grid information on a new directory
and use the following command:
8


antechamber -i electrostatic_grid.log -fi gout -c resp -nc 0 -m 1 -o
acetone.resp.prep -fo prepi -rn ACET


8
Run simply the commanu "antechambei" to have a shoit uesciiption of the meaning of all the
option iecognizeu by antechambei.
16
Actually, Antechamber recalls several programs in sequence which produce many
different intermediate files in your directory. When the process ends correctly you
should see the file acetone.resp.prep which is the file with the partial RESP charges
that we will use in the next step (copy it in a new directory and move to it).


5 – Water box

It is time to create the water box containing the acetone and the files necessary to run a
short classical Molecular Dynamics (MD) run. In fact, we want then to perform a
classical pre-equilibration of the system, in order to relax it near to a “stable state”.
9

For this aim we will use the Graphical User Interface Xleap of Amber10:

xleap -f /home/ippoliti/PROGRAMS/src/amber11/dat/leap/cmd/leaprc.ff99SB &

where the file leaprc.ff99SB is used to load all libraries which contains the parameters of
the Amber force field 99SB. Such a force field like any others has been tuned to
describe aminoacids, nucleic acids, etc but there is no information about acetone. For
this reason we have calculated the partial charges, which now we can load in Xleap by
typing the following command (in the Xleap main window):
10


loadamberprep acetone.resp.prep

and for the same reason some other parameters are still missing and have to be added
manually. Most of them can be retrieved by the “general Amber force field for organic
molecules GAFF”:

loadamberparams /home/ippoliti/PROGRAMS/src/amber11/dat/leap/parm/gaff.dat

other ones, however, have to provide manually. It is not difficult to calculate them but
here we will no explain how to do
11
. We have already prepared a file with such missing
parameters (above all bond and angles ones) and they can be load in Xleap by the
following command:

loadamberparams /work/Tutorial/ACETONE/5-XLEAP/acetone.frcmod

You can now give a look at your system by the command edit:

edit ACET

You can also check if all the parameters for the acetone have been loaded:

check ACET

Finally, you can save the topology and coordinates files for your ACET unit by typing:

9
Remembei the time step foi a classical NB iun is ~ps, while the time step foi a quantum NB is
~fs. So, the classical pie-equilibiation is essential since typical ielaxation times aie of the oiuei
of 1us-1uus of ps!
1u
The syntax foi any Xleap commanu can be iecall by typing the commanu without any
aiguments.
11
Refei to the Ambei manual, foi example.
17

saveamberparm ACET acetone.top acetone.rst

However, we want to study the acetone in water and therefore we need to solvate the
system, before:

solvatebox ACET TIP3PBOX 14

TIP3PBOX specifies that we solvate with the classical water model molecule
“TIP3P”
12
; an orthorhombic box whose walls are at least 14 Å from any acetone’s atoms
has been created:

edit ACET

From the new window you can also look at the partial charges and other parameters of
your system:

• Select the atoms
• Edit/Edit selected atoms

Finally, we save the topology and coordinates files for our solvated system:

saveamberparm ACET acetone_solv.top acetone_solv.rst

Copy the two files to another folder.
By the VMD software
13
you can visualize your system:

vmd –parm7 acetone_solv.top –rst7 acetone_solv.rst


6 – Pre Equilibration

We need now to equilibrate the system at force field level in order to later start the
QM/MM simulation from a configuration “not so far” from an equilibrium one (at the
QM/MM level).
To run MD simulation we will use the “sander” program of the AMBER10 package.
We proceed this way:
14


1. First, classical minimization of the system restraining the acetone molecule to
the initial position: this step is performed since the initial Xleap solvation is not
physically reasonable (no hydrogen bonds, etc) and this way we favour water
2. molecules to orient correctly around the acetone:


mpirun -np 8 sander.MPI -O -i 1-restraint.inp -o eq_restraint.out -c acetone_solv.rst \
-p acetone_solv.top -r eq_restraint.rst -ref acetone_solv.rst -inf eq_restraint.info &


12
http:¡¡en.wikipeuia.oig¡wiki¡Watei_mouel
1S
vNB 0sei's uuiue: http:¡¡www.ks.uiuc.euu¡Reseaich¡vmu¡cuiient¡ug¡
14
All the input file foi sanuei can be founu in the foluei:
¡woik¡Tutoiial¡ACET0NE¡6-SANBER
18
Note: the command “tail eq_restraint.info” can be used to monitor the
minimization and verify that it does not reach the max number of steps but stop before
satisfying the convergence criteria.

3. Then, a not constrained minimization is performed (single line command):

mpirun -np 8 sander.MPI -O -i 2-minimization.inp -o eq_minimization.out -c
eq_restraint.rst -p acetone_solv.top -r eq_minimization.rst -inf
eq_minimization.info &

4. Now, we take the system at 300 K with MD at constant volume and a linear
heating. In this step we constrain weakly acetone to the initial position so that
water can spread all around the acetone without forming “holes”. Since the liquid
water relaxation time is order of 10 ps we need to perform a > 10 ps MD:

mpirun -np 8 sander.MPI -O -i 3-heating.inp -p acetone_solv.top -c
eq_minimization.rst -ref eq_minimization.rst -o eq_heating.out -r eq_heating.rst -x
eq_heating.crd -e eq_heating.en -inf eq_heating.info &

5. Finally, we couple our system simultaneously to a thermostat at 300 K and a
barostat at 1 atm and perform an NPT simulation to let the density of the system
to reach the equilibrium value at room condition (~ 1g/cm
3
since the most is
formed by water):

mpirun -np 8 sander.MPI -O -i 4-eq_density.inp -p acetone_solv.top -c
eq_heating.rst -o eq_density.out -r eq_density.rst -x eq_density.crd -e
eq_density.en -inf eq_density.info &

Note: when the last step has ended, you can fast analyze the behavior of all the
physically relevant quantities of your system (like the density for example) by using
the perl script “process_mdout.perl”

(The perl-script is located in the sample subfolder 6-SANDER/analysis)

Box Density


mkdir analysis
cd analysis
process_mdout.perl ../eq_density.out
xmgrace summary.DENSITY






Why is density smaller than 1g/cm
3
?

VMD visualization:

Final coordinates: vmd –parm7 acetone_solv.top –rst7 “outputfile”.rst
Trajectory: vmd –parm7 acetone_solv.top –crdbox “outputfile”.crd


19
7 – Reimaging

Let’s give a look at the last configuration you obtained from the classical molecular
dynamics equilibration:

cd ..
vmd -parm7 acetone_solv.top -rst7 eq_density.rst

What did happen to our orthorhombic box?



The image shows your system without applying the periodic boundary conditions
(PBC) that sander and all the other programs of Amber10 use. So, molecules drift
over time and may span multiple periodic cells; this is normal when you are working
on Amber10 or on some other molecular dynamics package. However, now we want
to move to CPMD in order to perform a QM/MM MD simulation, and CPMD does
not apply “automatically” PBC. Consequently, we need to “reimage” the coordinates
into the primary unit cell. We can use the “ptraj” program
15
of the Amber10 suite to
accomplish this task. Move the topology and coordinates files to another folder and
then create the input file eq_density.ptraj for ptraj:

trajin eq_density.rst ! coordinates file to read
trajout eq_density_reimaged.rst restart ! output file in the same format as the input
center :1 ! center the box to the geometric center of residue 1
image center ! force all the molecules into the primary unit cell

Run ptraj according this syntax:

ptraj acetone_solv.top < eq_density.ptraj

Verify that the imaging has been correctly done:

vmd -parm7 acetone_solv.top -rst7 eq_density_reimaged.rst.1


1S
http:¡¡ambeimu.oig¡uoc1u¡AmbeiTools.puf
2u



8 – Convert MD files

Copy the topology and the “reimaged” coordinates files to a new directory and typing
the following command:

Conv_7.x acetone_solv.top eq_density_reimaged.rst.1 solvate

Conv_7.x is an in-house program written to convert the Amber MD files in the
GROMOS format. This because the QM/MM interface of CPMD works with such a
format. The option “solvate” let us specify that the water molecules should be treated
as solvent ones: this is useful only if you are interested to read in the log files of
CPMD energies and other quantities partitioned in solute and solvent components.

The converter will produce 5 files:

• gromos.top the Gromos topology file for our system
• gromos.inp the Gromos input file
• gromos.g96 the coordinates file in g96 format
• gromacs.top the Gromacs topology file
• ffgro96.itp the itp file for the Gromacs software

We need only the first 3 files, but some changes
16
have to be done in order to
correctly set up a QM/MM MD simulation:

Changes in gromos.inp

1 - In the section SYSTEM the two numbers should be in sequence:

Number of (identical) solute (not necessarily the QM part!) molecules
Number of (identical) solvent (not necessarily the MM part!) molecules

Such information can be retrieved, for example, by typing on the prompt
command line:

tail gromacs.top

16
see also http:¡¡www.cpmu.oig¡manual¡noue267.html
21

2 - In the section BOUNDARY:

The first number should be 0 for isolated system; >0 if PBC in parallelepiped
box has been used; <0 if PBC in octahedric box has been used.
The following 3 numbers are the sizes of the box that can be read at the end of
gromos.g96 file.
90.0 is the angle between the x and z axis of the box.
The last number is ignored by CPMD in QM/MM simulations.

3 - In the section SUBMOLECULES the numbers in sequence should be:

Number of (different) solute molecules.
Index of the last atom of the first solute molecule.
Index of the last atom of the second solute molecule.
...

Such data can be read from the file gromos.g96:

vi gromos.g96

4 - In the section PRINT you could want to modify the first number which give
you the number of steps after that CPMD write info of the energy in the output
file (20 is usually enough).

5 - In the section FORCE, under the line of 1's (which turns the various force
components on), we have to put:

The number of different layers, usually 2 (Solute and solvent)
Index of the last atom of layer 1
Index of the last atom of layer 2
...

Changes in gromos.top

In the section ATOMTYPENAME replace the names of the types of the atoms,
from the standard generic force field library "gaff":

vi $AMBERHOME/dat/leap/parm/gaff.dat

to the Amber force field library:

vi $AMBERHOME/dat/leap/parm/parm99.dat

The correctly modified files gromos_mod.top and gromos_mod.inp can be found in:

/work/Tutorial/ACETONE/8-Conv_7



22
9 – QM/MM MD

Copy the modified files and the gromos.g96 file to a new directory.

At this point, we have all the files which describe the MM part and its interactions;
the last step will be to write the input file for CPMD with the instructions for the
simulation and the definition of the QM part. A CPMD input file for a QM/MM
simulation is similar to the CPMD input file for a standard QM calculation which has
been described in paragraph 2 (section &INFO, &CPMD, &SYSTEM, &ATOMS,
&DFT). However, there are 6 main differences which should always be taken into
account when you deal with the QM/MM interface of CPMD:

1. In the &CPMD section the keyword QMMM has to be added.
2. A new &QMMM section, which we will explain in detail below, is
mandatory.
3. The QM atoms are specified in the &ATOMS section similar to normal
CPMD calculations. Instead of explicit coordinates one has to provide the
atom index as given in the Gromos topology and coordinates files:
vi gromos.g96
4. The keyword ANGSTROM in the &SYSTEM section cannot be used, so any
length has to be specified in a.u.
5. The option ABSOLUTE in the keyword CELL cannot be used. Therefore the
correct syntax for the size of the rectangular box AxBxC is

A B/A C/A 0 0 0

6. The QM system in a QM/MM calculation can only be dealt as isolated system,
i.e. without explicit PBC since there is the MM environment all round it.
Even though we are requesting an isolated system calculation (SYMMETRY
keyword with the option ISOLATED SYSTEM or 0), the calculation is, in
fact, still done in a periodic cell (we are still using plane wave basis set!).
Since acetone has a dipole moment, we have to take care of the long range
interactions between periodic images and there are methods (activated with
the keyword POISSON SOLVER in the &SYSTEM section) implemented in
CPMD to compensate for this effect. We will choose the TUCKERMAN
Poisson solver
17
since it has been proven to be the most effective one with
typical systems studied in biology. Decoupling of the electrostatic images in
the Poisson solver requires to increase the box size over the dimension of the
molecule: practical experience shows that 3.5 Å space between the outmost
atoms and the box is usually sufficient for typical biological systems.

&QMMM section

In this paragraph we will review the most relevant keywords to specify in the
&QMMM section of the CPMD input file. See for example
18
for a complete
list:

17
G.J. Martyna and M. E. Tuckerman, J. Chem. Phys. 110, 2810 (1999).
18
http:¡¡www.cpmu.oig¡manual¡noue2S8.html
2S
TOPOLOGY: On the next line the name of a Gromos topology file
has to be given.
COORDINATES: On the next line the name of a Gromos96 format
coordinate file has to be given.
INPUT: On the next line the name of a Gromos input file has to
be given.
AMBER: An Amber functional form for the classical force field
is used.
ELECTROSTATIC
COUPLING: The electrostatic interaction of the quantum system
with the classical system is explicitly kept into account
for all classical atoms at a distance r ! RCUT_NN
from any quantum atom and for all the MM atoms at a
distance of RCUT_NN < r ! RCUT_MIX and a
charge larger than 0.1e (NN atoms). MM-atoms with a
charge smaller than 0.1e and a distance of RCUT_NN
< r ! RCUT_MIX and all MM-atoms with
RCUT_MIX < r ! RCUT_ESP are coupled to the
QM system by a ESP coupling Hamiltonian (EC
atoms).

If the additional LONG RANGE keyword is specified,
the interaction of the QM-system with the rest of the
classical atoms is explicitly kept into account via
interacting with a multipole expansion for the QM-
system up to quadrupolar order. A file named
MULTIPOLE is produced.

If LONG RANGE is omitted the quantum system is
coupled to the classical atoms not in the NN-area and
in the EC-area list via the force-field charges.

If the keyword ELECTROSTATIC COUPLING is
omitted, all classical atoms are coupled to the quantum
system by the force-field charges (mechanical
coupling): computational expensive calculation!

RCUT_NN: The cutoff distance for atoms in the nearest neighbor
region from the QM-system is read from the next line.
We will use the default value of 10 a.u.
RCUT_MIX: The cutoff distance for atoms in the intermediate
region is read from the next line. We will use the value
of 15 a.u.
RCUT_EXP: The cutoff distance for atoms in the ESP-area is read
from the next line. We will use the value of 20 a.u.
UPDATE LIST: On the next line the number of MD steps between
updates of the various lists of atoms for
ELECTROSTATIC COUPLING is given. At every list
update a file INTERACTING_NEW.pdb is created
(and overwritten).
24
SAMPLE
INTERACTING: The sampling rate for writing a trajectory of the
interacting subsystem is read from the next line. With
the additional keyword OFF or a sampling rate of 0,
those trajectories are not written.
ARRAYSIZES: Parameters for the dimensions of various internal arrays
can be given in this block. The syntax is one label and
the according dimension per line. The suitable
parameters can be estimated using the script
estimate_gromos_size.sh:

estimate_gromos_size.sh gromos_mod.top

This section of the input has to be terminated by a line
containing END ARRAYSIZES.

Now, we have all the elements to write a CPMD input file for a QM/MM simulation.
But which steps do we need to perform a stable Car-Parrinello MD?
We have the equilibrated coordinates at room conditions obtained from a classical MD:
this is a good starting point, however we still need to equilibrate the system at QM/MM
level since the two levels of theory are different.

Therefore, as we have done in the second paragraph, we should at first optimize the
geometry of the system. Unfortunately, all the optimizer algorithms in CPMD do not
work together with the QM/MM interface. Consequently, we have to use some “trick”
to find a minimal energy structure (at QM/MM level). In particular in this tutorial we
will perform a simulated annealing (keyword ANNEALING IONS), i.e. we run a CP-
dynamics where and gradually removing kinetic energy from the nuclei by multiplying
velocities with a factor (in our case it is set to 0.99, so 1% of the kinetic energy will be
removed in every step). Here it is the annealing.inp file which perform this
preliminary step:

&QMMM
TOPOLOGY
gromos_mod.top
COORDINATES
gromos.g96
INPUT
gromos_mod.inp
ELECTROSTATIC COUPLING LONG RANGE
RCUT_NN
10
RCUT_MIX
15
RCUT_ESP
20
UPDATE LIST
100
SAMPLE_INTERACTING
0
AMBER
ARRAYSIZES

MAXATT 16
MAXAA2 11
MAXNRP 20
MAXNBT 15
MAXBNH 16
MAXBON 13
MAXTTY 14
2S
MXQHEH 22
MAXTH 13
MAXQTY 10
MAXHIH 10
MAXQHI 10
MAXPTY 14
MXPHIH 28
MAXPHI 11
MAXCAG 11
MAXAEX 20024
MXEX14 22

END ARRAYSIZES
&END

&CPMD
QMMM
MOLECULAR DYNAMICS CP
ISOLATED MOLECULE
QUENCH BO
ANNEALING IONS
0.99
TEMPERATURE
300
EMASS
600.
TIMESTEP
5.0
MAXSTEP
10000
TRAJECTORY SAMPLE
0
STORE
100
RESTFILE
1
&END

&SYSTEM
POISSON SOLVER TUCKERMAN
SYMMETRY
0
CELL
18.61 1.11 0.95 0 0 0
CUTOFF
70.
CHARGE
0.0
&END

&DFT
FUNCTIONAL BLYP
&END

&ATOMS
*H_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=S
6
4 5 6 8 9 10

*C_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=P
3
2 3 7

*O_MT_BLYP.psp KLEINMAN-BYLANDER
LMAX=P
1
1
&END


Some comments on the keywords in the &CPMD section which are not explained, yet:

26
MOLECULAR DYNAMICS CP: Perform a molecular dynamics run.
CP stands for a Car-Parrinello type of MD.
ISOLATED MOLECULE: Calculate the ionic temperature assuming that
the system consists of an isolated molecule or
cluster.
QUENCH BO: the wavefunction is converged at the
beginning of the MD run.
TEMPERATURE: The initial temperature for the atoms in Kelvin
is read from the next line: we start from 300 K
since it is the temperature at which we
equilibrate the system classically.
EMASS: The fictitious electron mass in atomic units for
the CP dynamics is read from the next line.
We choose 600 a.u. but ideally a careful set of
tests should be done to verify that adiabaticity
conditions to be met
19
: this and the following
one are the only parameters to tune in order to
decouple the electronic and ionic degrees of
freedom and minimize their energy transfer.
TIMESTEP: The time step in atomic units is read from the
next line. We use the default time step of 5 a.u.
~ 1.2 fs.
MAXSTEP: The maximum number of steps for molecular
dynamics to be performed. The value is read
from the next line.
TRAJECTORY SAMPLE: Store the atomic positions, velocities and
optionally forces at N every time step on the
TRAJECTORY file. N is read from the next
line. If N=0 the trajectory file will not be
written.
STORE: The RESTART file is updated every N steps.
N is read from the next line. Default is at the
end of the run.
RESTFILE: The number of distinct RESTART files
generated during CPMD runs is read from the
next line. The restart files are written in turn.
Default is 1.

Moreover, here it is a simple procedure to obtain the sizes of the box to insert under the
CELL keyword by using standard bash commands:

• Create a file with the coordinate of the atoms belong to the QM part:

grep CET gromos.g96 > QM.coor

• Reorder the lines in the column 5 (6,7) for the coordinate x (y,z) with an
increasing numerical (-n) order:
sort -k 5 -n QM.coor


19
http:¡¡www.theochem.iuhi-uni-bochum.ue¡ieseaich¡maix¡maix.puf
27
• Take the last value (L) of the column (in nm), subtract it to the first (F) one,
add 0.7 nm (i.e. 2 * 3.5 Å for the Poisson solver’s requirements) and then
convert it to a.u.:

echo "(L - F + 0.7)*10/0.529" | bc –l

• Finally remember that under the CELL keyword of the CPMD input file the
size of the quantum cell will be inserted according to the syntax:

size_x size_y/size_x size_z/size_x 0 0 0


1 - ANNEALING

We are now ready to run the annealing (copy all the file in a folder called
ANNEALING):

mpirun -np 8 cpmd.x annealing.inp
/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > annealing.out &

While the simulation proceeds you can monitor the decreasing temperature (third
column named TEMPP) this way:

tail -f annealing.out

When the temperature reaches about 2-4 K we can “softly” stop the calculation (that
is in order to make it write a RESTART file) by typing on the prompt line:

touch EXIT

The final configuration will be stored in the RESTART.1 file.
More files will be generated during a QM/MM CP simulation:

QMMM_ORDER The first line specifies the total number of atoms (NAT) and the
number of quantum atoms (NATQ). The subsequent NAT lines
contain, for every atom, the gromos atom number, the internal
CPMD atom number, the CP species number isp and the
number in the list of atoms for this species NA(isp). The
quantum atoms are specified in the first NATQ lines.

CRD_INI.g96 Contains the positions of all atoms in the first frame of the
simulation in Gromos extended format (g96).

CRD_FIN.g96 Contains the positions of all atoms in the last frame of the
simulation in Gromos extended format (g96).

INTERACTING.pdb Contains (in a non-standard PDB-like format) all the QM atoms
and all the MM atoms in the electrostatic coupling NN list. The
5-th column in this file specifies the gromos atom number as
defined in the topology file and in the coordinates file. The 10-
th column specifies the CPMD atom number as in the
TRAJECTORY file. The quantum atoms are labeled by the
residue name QUA.
28

INTERACTING_NEW.pdb The same as before, but it is created if the file
INTERACTING.pdb is detected in the current working
directory of the CPMD run.

MM_CELL_TRANS The QM system (atoms and wavefunction) is always re-
centered in the given supercell. This file contains, the
trajectory of the re-centering offset for the QM-box. The first
column ist the frame number (NFI) followed by the x-, y-, and
z-component of the cell-shift vector.

ENERGIES Contains all the energies along the trajectory.


Let’s give a closer look at the output file annealing.out which present some new
sections:

CAR-PARRINELLO MOLECULAR DYNAMICS

PATH TO THE RESTART FILES: ./
ITERATIVE ORTHOGONALIZATION
MAXIT: 30
EPS: 1.00E-06
MAXIMUM NUMBER OF STEPS: 10000 STEPS
MAXIMUM NUMBER OF ITERATIONS FOR SC: 10000 STEPS
PRINT INTERMEDIATE RESULTS EVERY 10001 STEPS
STORE INTERMEDIATE RESULTS EVERY 100 STEPS
STORE INTERMEDIATE RESULTS EVERY 10001 SELF-CONSISTENT STEPS
NUMBER OF DISTINCT RESTART FILES: 1
TEMPERATURE IS CALCULATED ASSUMING AN ISOLATED MOLECULE

In CPMD, atoms are frequently referred to as ions, which may be confusing. This is
due to the pseudopotential approach, where you integrate the core electrons into the
(pseudo)atom which then could be also described as an ion. See for example the
following output segment:

FICTITIOUS ELECTRON MASS: 600.0000
TIME STEP FOR ELECTRONS: 5.0000
TIME STEP FOR IONS: 5.0000
QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE
SIMULATED ANNEALING OF IONS WITH ANNERI = 0.990000
ELECTRON DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED
ION DYNAMICS: THE TEMPERATURE IS NOT CONTROLLED

This part of the output tells us, that the TIMESTEP keyword was recognized as well
as the output option and that there will be no temperature control, i.e. we will do a
microcanonical (NVE-ensemble) simulation.

Then, several sections devoted to describe in detail the QM/MM interface and its data
immediately follow:

INITIALIZATION TIME: 1.05 SECONDS

*** MDPT| SIZE OF THE PROGRAM IS 95528/ 288728 kBYTES ***
*** PHFAC| SIZE OF THE PROGRAM IS 97076/ 300980 kBYTES ***
*** ATOMWF| SIZE OF THE PROGRAM IS 98100/ 302796 kBYTES ***
ATRHO| CHARGE(R-SPACE): 24.000000 (G-SPACE): 24.000000

RE-CENTERING QM SYSTEM AT EVERY TIME STEP

BOX TOLERANCE [a.u.] 7.00000000000000

BOX SIZE [a.u.] QM SYSTEM SIZE [a.u.]
X DIRECTION: CELLDIM = 18.6100; XMAX-XMIN= 5.3773
29
Y DIRECTION: CELLDIM = 20.6571; YMAX-YMIN= 7.3868
Z DIRECTION: CELLDIM = 17.6795; ZMAX-ZMIN= 4.3595

>>>>>>>> QUENCH SYSTEM TO THE BORN-OPPENHEIMER SURFACE <<<<<<<<

*** QUENBO| SIZE OF THE PROGRAM IS 112180/ 308536 kBYTES ***
*** MM_ELSTAT| SIZE OF THE PROGRAM IS 112288/ 308536 kBYTES ***

!!!!!!!!!!!!!!!!!! WARNING !!!!!!!!!!!!!!!!!!!
THE QM SYSTEM DOES NOT HAVE AN INTEGER CHARGE.
A COMPENSATING CHARGE OF 0.000040 HAS BEEN
DISTRIBUTED OVER THE NN ATOMS.
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!



0.000040 e of charge to compensate: for all practical purposes this is zero!

After the force initialization section finally the MD begins:

NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU
1 0.00006 297.0 -54.34715 -51.01094 -51.01088 -36.46342 0.218E-04 1.53
2 0.00056 293.9 -54.34671 -51.04477 -51.04421 -36.46309 0.863E-04 1.54
3 0.00136 290.9 -54.34661 -51.07860 -51.07724 -36.46309 0.191E-03 1.52
4 0.00201 287.9 -54.34663 -51.11193 -51.10992 -36.46319 0.335E-03 1.52
...

The individual columns have the following meaning:

NFI Step number (number of finite iterations)

EKINC Fictitious kinetic energy of the electronic degrees of freedom

TEMPP Temperature (= kinetic energy / degrees of freedom) for atoms
(ions)

EKS Kohn-Sham energy; equivalent to the potential energy in
classical MD

ECLASSIC The total energy in a classical MD, but not the conserved
quantity for CP-dynamics (ECLASSIC = EHAM - EKINC).

EHAM Energy of the total CP-Hamiltonian; the conserved quantity.

EQM Energy of QM part (electrons + nuclei contribution)

DIS Mean squared displacement of the atoms from the initial
coordinates.

TCPU Time needed for this step

Finally we get a summary of some averages and root mean squared deviations for
some of the monitored quantities. This is quite useful to detect unwanted energy drifts
or too large fluctuations in the simulation:

RESTART INFORMATION WRITTEN ON FILE ./RESTART.1

****************************************************************
* AVERAGED QUANTITIES *
****************************************************************
Su
MEAN VALUE +/- RMS DEVIATION
<x> [<x^2>-<x>^2]**(1/2)
ELECTRON KINETIC ENERGY 0.000867 0.300539E-03
IONIC TEMPERATURE 37.2640 52.8318
DENSITY FUNCTIONAL ENERGY -56.788301 0.907159
CLASSICAL ENERGY -56.369667 1.48329
CONSERVED ENERGY -56.368800 1.48357
NOSE ENERGY ELECTRONS 0.000000 0.00000
NOSE ENERGY IONS 0.000000 0.00000
CONSTRAINTS ENERGY 0.000000 0.00000
RESTRAINTS ENERGY 0.000000 0.00000
ION DISPLACEMENT 0.306287 0.932230E-01
CPU TIME 1.5641


2 – TEST

To verify that the reached configuration is physically "reasonable", a good test is to
run a simulation in a NVE ensemble and monitoring the temperature (column 3) and
the physical energy (column 5): if after some steps these two quantities stabilize
(usually oscillating around a value of temperature smaller than 100 K) then we can be
confident that the RESTART.1 file previously obtained is a good minimal energy
structure. On the other hand, if energy and/or temperature continuously increase that
means we have not a good structure and another annealing procedure is required by
starting from another point (for example after heating the system at 300 K in order to
move the system away from that “wrong” energy potential basin). The test can be
accomplished by the following procedure:

• Create a new folder:

mkdir TEST
cd TEST
• Copy the following files from the previous calculation:

cp ../gromos* .
cp ../RESTART.1 RESTART
cp ../annealing.inp test.inp

• Modify the test.inp file in order to change the &CPMD section so as to
appear:

&CPMD
RESTART COORDINATES VELOCITIES WAVEFUNCTION
QMMM
MOLECULAR DYNAMICS CP
ISOLATED MOLECULE
EMASS
600.
TIMESTEP
5.0
MAXSTEP
3000
TRAJECTORY SAMPLE
0
&END

S1
Note: in the RESTART line there is no LATEST option: this way CPMD
expects to read data from a file named exactly “RESTART”.

• Run the test:

mpirun -np 8 cpmd.x test.inp
/home/ippoliti/PROGRAMS/src/cpmd3.13.2/PP > test.out &

• Monitor the simulation:

tail –f test.out

• When it ends you can plot on a graph the temperature and the physical energy
by gnuplot:



gnuplot
p 'ENERGIES' u 1:3 w l
p 'ENERGIES' u 1:5 w l
quit



3 – HEATING

If the test went well, we can come back to the configuration obtained by annealing
and start heating the system to room temperature. There are several methods
implemented in CPMD to do that. We choose to increase the target temperature of a
thermostat (coupled to the system) linearly at each step by performing a usual CP
dynamics. A simple Berendsen-type thermostat
20
will be applied.
Two more keywords are required in &CPMD section with respect to the previous
input file:

1. TEMPERATURE with the option RAMP; 3 numbers have to be specified on
the line below the keyword: initial and target temperature in K and the
ramping speed in K per atomic time unit (to get the change per timestep you
have to multiply it with the value of TIMESTEP). Read the initial temperature
from the output file of the annealing procedure.

2. BERENDSEN with the option IONS; 2 numbers has to be specified on the
line below the keyword: the target temperature (the initial one in our case) and
the time constant ! in a.u. (0.12 ps is a reasonable value).

The procedure to accomplish the heating can be summarized this way:

2u
B. }. C. Beienusen, }. P. N. Postma, W. F. van uunsteien, A. BiNola, }. R. Baak
}. Chem. Phys, 81, S684 (1984).
S2

• Create a new folder:

mkdir HEATING
cd HEATING

• Copy the following files from the previous calculation:

cp ../ANNEALING/gromos* .
cp ../ANNEALING/RESTART.1 RESTART
cp ../TEST/test.inp heating.inp

• Modify heating.inp: vi heating.inp
Include the following lines in the &CPMD section:

BERENDSEN IONS
3.8 1000
TEMPERATURE RAMP
3.8 340.0 1

• Monitor the temperature: tail –f heating.out

• If the temperature reach approximately the target temperature even before the
MAXSTEP number of steps are performed you can stops the simulation:

touch EXIT


4 – PRODUCTION RUN

We aie finally ieauy to iun a CP moleculai uynamics in ioom conuitions.
To uo that, as usual, we will cieate a new foluei:

mkdir PRODUCTION-RUN
cd PRODUCTION-RUN

and then we will copy the necessary files there in order to start the calculation from
the last configuration got from the heating procedure:

cp ../HEATING/gromos* .
cp ../HEATING/RESTART.1 RESTART
cp ../HEATING/heating.inp cpmd.inp

To run CP molecular dynamics we need to modify the previous input file:

• We want to restart from previous wavefunction, coordinates and velocities
since we want to conserve the temperature information from the RESTART
file. Therefore we will preserve the option VELOCITIES in the RESTART
keyword and we will remove TEMPERATURE keyword.
SS
We will replace the Berendsen thermostat with the Nose-Hoover chains
21
: this
because the second kind of thermostat preserves the Maxwell distribution of
the velocities and so it is more physically meaningful. In more technical
words, it provides an NVT ensemble for a system in equilibrium.
The keyword that turns it on is NOSE, and then you have to specify the
degrees of freedom to which you want to apply it (IONS); the target
temperature in Kelvin and the thermostat frequency in cm-1 are read from the
next line:

NOSE IONS
300 4000

For the choice of frequency at which the energy transfer happens, you have
only to pay attention not to select a resonance vibrational frequency of your
system.

• We will reintroduce the keyword MAXSTEP to perform 10000 steps (or more
if you have time: typical CPMD trajectories nowadays are tens of ps long!)
• Finally, we want to save 10 restart files (i.e. configurations from which we
will calculate the dipole moment of acetone) equally separated in time along
the trajectory. We can do that by properly using the keyword RESTFILE and
STORE:

STORE
100
RESTFILE
10

This way CPMD will create ten restart files in sequence called RESTART.1,
RESTART.2, …, RESTART.10 each one after 1000 steps of dynamics.

Running meaningful Car-Parrinello dynamics simulation requires adiabaticity
conditions to be met, i.e. the separation of the electronic and ionic degrees of
freedom.
Theoretically such separation can be achieved by separating the power spectrum of
the orbital classical fields from the phonon spectrum of the ions (the gap between the
lowest electronic frequency and the highest ionic frequency should be large enough).
Since the electronic frequencies depend on the fictitious electron mass EMASS one
should carefully optimize its value and rise the lowest frequency appropriately.
The adiabaticity can be observed by running test simulations and looking at the
energy components.
In particular, the fictitious kinetic energy of the electronic degrees of freedom
(EKINC, second column in the ENERGIES file) might have a tendency to grow.
However, after an initial transfer of a little kinetic energy, the electrons should be
much “colder" than the ions, since only then will the electronic structure remain close
to the Born-Oppenheimer surface and thus the wavefunction and forces derived from
it will be meaningful. Therefore, we must always monitor the behavior of the EKINC

21
S. Nosé anu N. L. Klein, Nol. Phys. Su, 1uSS (198S); S. Nosé, Nol. Phys. S2, 2SS (1984); S. Nosé,
}. Chem. Phys. 81, S11 (1984); S. Nosé, Piog. Theoi. Phys. Suppl. 1uS, 1 (1991); W. u. Boovei,
Phys. Rev. A S1, 169S (198S).
S4
in order to verify the system keeps being in the adiabatic regime:

TOTAL INTEGRATED ELECTRONIC DENSITY
IN G-SPACE = 24.000000
IN R-SPACE = 24.000000

(K+E1+L+N+X+Q+M) TOTAL ENERGY = -57.87866446 A.U.
(K+E1+L+N+X) TOTAL QM ENERGY = -36.47942711 A.U.
(Q) TOTAL QM/MM ENERGY = 0.00000000 A.U.
(M) TOTAL MM ENERGY = -21.38112962 A.U.
DIFFERENCE = -0.01810773 A.U.
(K) KINETIC ENERGY = 27.71754549 A.U.
(E1=A-S+R) ELECTROSTATIC ENERGY = -27.62122216 A.U.
(S) ESELF = 29.92067103 A.U.
(R) ESR = 1.68558813 A.U.
(L) LOCAL PSEUDOPOTENTIAL ENERGY = -29.41090607 A.U.
(N) N-L PSEUDOPOTENTIAL ENERGY = 3.57237860 A.U.
(X) EXCHANGE-CORRELATION ENERGY = -10.73722297 A.U.
GRADIENT CORRECTION ENERGY = -0.58313547 A.U.

NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU
1 0.00001 302.5 -57.87866 -54.48084 -54.48082 -36.47943 0.538E-05 1.50
2 0.00011 302.3 -57.87721 -54.48093 -54.48082 -36.47936 0.214E-04 1.47
3 0.00027 302.2 -57.87578 -54.48109 -54.48082 -36.47937 0.480E-04 1.35
4 0.00037 302.0 -57.87431 -54.48118 -54.48081 -36.47937 0.849E-04 1.50
5 0.00039 301.9 -57.87280 -54.48119 -54.48080 -36.47937 0.132E-03 1.35
6 0.00039 301.8 -57.87125 -54.48118 -54.48079 -36.47937 0.190E-03 1.35
7 0.00037 301.6 -57.86966 -54.48116 -54.48078 -36.47937 0.258E-03 1.67
8 0.00037 301.5 -57.86803 -54.48115 -54.48078 -36.47936 0.336E-03 1.35
9 0.00037 301.3 -57.86636 -54.48114 -54.48077 -36.47936 0.425E-03 1.46
NBPML: 80733 ELEMENTS IN THE PAIRLIST
10 0.00037 301.2 -57.86466 -54.48114 -54.48077 -36.47935 0.523E-03 1.37
11 0.00036 301.0 -57.86291 -54.48113 -54.48077 -36.47934 0.632E-03 1.46
12 0.00035 300.9 -57.86112 -54.48111 -54.48076 -36.47932 0.752E-03 1.35
13 0.00035 300.7 -57.85927 -54.48107 -54.48073 -36.47931 0.881E-03 1.35
14 0.00034 300.5 -57.85740 -54.48106 -54.48072 -36.47929 0.102E-02 1.46
15 0.00033 300.4 -57.85551 -54.48106 -54.48073 -36.47928 0.117E-02 1.35
16 0.00032 300.2 -57.85357 -54.48105 -54.48073 -36.47927 0.133E-02 1.46
17 0.00031 300.0 -57.85159 -54.48103 -54.48072 -36.47926 0.150E-02 1.35
18 0.00030 299.8 -57.84956 -54.48101 -54.48070 -36.47925 0.169E-02 1.51
19 0.00030 299.7 -57.84751 -54.48099 -54.48070 -36.47924 0.188E-02 1.42










Ensuring adiabaticity of CP dynamics consists of decoupling the two subsystems and
thus minimizing the energy transfer from ionic degrees of freedom to electronic ones.
In this sense the system during CP dynamics simulation should be kept in a
metastable state.

*"+,: any time you notice something stiange (anu even if you uo not!) I veiy
useful suggestion is ALWAYS look at youi simulations by some visualization tool:
the most of the pioblem aie immeuiately iuentifieu at a glance.
To visualize a CP-NN simulation you can use vmu
22
:

vmd -g96 CRD_INI.g96 -cpmd TRAJECTORY

22
Any commanu of vmu can be also execute by the u0I of the piogiam: iefei to its manual foi
uetails.
SS



5 – DIPOLE CALCULATION

As a last step we want to calculate the uipole moment foi each snapshot saveu in
ten iestaits file pieviously collecteu anu then make the mean value in oiuei to
give this way an estimate of the tempeiatuie anu entiopic effects uue to the
enviionment foimeu by the solvent.

Cieate a new foluei anu copy the iestait files anu the othei neeueu files in this
uiiectoiy:

mkdir DIPOLE_CALCULATION
cp ../ PRODUCTION-RUN/RESTART.* .
cp ../ PRODUCTION-RUN/gromos* .
cp ../ PRODUCTION-RUN/cpmd.inp dipole.inp
cp ../PRODUCTION-RUN/LATEST .

anu mouify the input file to calculate the uipole moment as you have leaint in the
seconu paiagiaph:

.

&CPNB
QNNN
RESTART WAvEF0NCTI0N C00RBINATES LATEST
PR0PERTIES
RESTFILE
u
&ENB


&PR0P
BIP0LE N0NENT
&ENB

.

The keywoiu LATEST is inseiteu in oiuei to peifoim the ten calculations in a
comfoitable way: in fact, if you want CPNB ieau the RESTART.X file you only
neeu to ieplace that name in the fiist line of the file LATEST. The keywoiu
RESTFILE with value u guaiantees that CPNB uoes not wiite a RESTART file at
the enu of each calculation (we uo not neeu it, now), so avoiuing it oveiwiites the
ones we have copieu fiom the PR0B0CTI0N-R0N foluei.
So, you can peifoim the following sequence of veiy fast calculations (less than S
sec!), being caieful to mouify the name in the fiist line of the file LATEST each
time:

mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole1.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole2.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole3.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole4.ouL &
S6
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole3.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole6.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole7.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole8.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole9.ouL &
mplrun -np 8 cpmd.x dlpole.lnp /home/lppollLl/Þ8CC8AMS/src/cpmd3.13.2/ÞÞ > dlpole10.ouL &

Note: you coulu have skippeu this pioceuuie by using the keywoiu

DIPOLE DYNAMICS SAMPLE
1000
in the pievious CP calculation. Such a keywoiu makes CPNB save the
cooiuinates of the uipole moments eveiy 1uuu steps on a file calleu BIP0LE. An
example is saveu in the foluei:

/work/Tutorial/ACETONE/9-CPMD-MM/4-PRODUCTION-RUN/DIPOLE/

Bowevei, these values aie polaiizations (in a.u.): they have to be multiply by the
volume to obtain the coiiect values of the uipole in a.u.

At this point you have only to extiact each value of the uipole moment:

grep -B 1 -A 4 "X Y" dipole1.out
grep -B 1 -A 4 "X Y" dipole2.out


anu calculate the aiithmetic mean B.

What is the uiffeience with iespect the value in vacuum we calculate in the
seconu paiagiaph.

What is the qualitative ieason of such a uiffeience.

The solvent effect can be sepaiateu in two uiffeient components: the
geometiy vaiiation of the solute with iespect to the gas phase (tempeiatuie
effect), anu the uiffeient polaiization of the wavefunction.
Bow coulu you pioceeu if you wanteu to iuentify the contiibution of the two
paits.