Basic usage of QM/MM in CPMD

Carme Rovira
Universitat de Barcelona (UB) &
Institució Catalana de Recerca i Estudis Avançats (ICREA)

1
 The CPMD code
(www.cpmd.org)
• Based on the original code by Car and Parrinello [1].

It is a production code with many unique features written in Fortran 77/90 with
about 150,000 lines of code (in 2005). The code is parallelized using MPI and
OpenMP.

• Since January of 2002 the program is freely available for non-commercial use [2].

[1] Car, R.; Parrinello, M.: Unified Approach for Molecular Dynamics and Density-Functional Theory.
Phys. Rev. Lett. 55 (1985) 2471–2474.
[2] CPMD V4.1 Copyright IBM Corp 1990–2004, Copyright MPI für Festkörperforschung Stuttgart
1997–2001, see also www.cmpd.org

See also:
J. Hutter and M. Iannuzzi. CPMD: Car-Parrinello molecular dynamics.
Z. Kristallogr. 220 (2005) 549–551
J. Hutter. Car-Parrinello molecular dynamics. WIREs Comput Mol Sci 2012, 2:604-612.
D. Marx, J. Hutter, Ab Initio Molecular Dynamics. Basic Theory and Advanced Methods.
Cambridge University Press. 2012
 Structure of the CPMD input file
SECTIONS
&CPMD

&END

&SYSTEM

&END

&DFT

&END

&ATOMS

&END
 Structure of the CPMD input file
“minimum” &CPMD contents
&CPMD
OPTIMIZE WAVEFUNCTION E = min E [ρ(r), {R I }]
&END ρ(r)

occ. 2
ρ(r) = ∑ ψi (r)
dumps out RESTART.1 and LATEST files i

∑ ci (G) exp[iG.r]
ψi (r )=
1
ΩG
./LATEST

Contains the path for

the restart file
 Structure of the CPMD input file
“minimum” &CPMD contents
&CPMD
OPTIMIZE WAVEFUNCTION E = min E [ρ(r), {R I }]
&END ρ(r)

&CPMD
OPTIMIZE GEOMETRY
RESTART WAVEFUNCTION LATEST
&END RESTART.1 and
LATEST files are
altogether always dumped out

&CPMD
OPTIMIZE WAVEFUNCTION GEOMETRY
&END
Structure of the CPMD input file:
The CPMD section
&CPMD
MOLECULAR DYNAMICS
RESTART WAVEFUNCTION COORDINATES LATEST
&END

&CPMD
MOLECULAR DYNAMICS
RESTART WAVEFUNCTION COORDINATES VELOCITIES LATEST
quench electrons bo In small letters => not used
RESTART ACCUMULATORS LATEST
&END
You can also restart other quantities (not covered in this
tutorial)
RESTART NOSEP NOSEE CELL LATEST
 Structure of the CPMD input file:
The CPMD section
(similar input as the one we’ll work
&CPMD during the afternoon practicals)
MOLECULAR DYNAMICS
RESTART WAVEFUNCTION COORDINATES VELOCITIES LATEST
MIRROR
LSD
minimize the density fuctional before
QUENCH ELECTRONS BO
starting the MD simulation
ODIIS
E = min E [ρ(r), {R I }]
4 ρ(r)
TIMESTEP
5.0 Time step, in a.u.
EMASS (1 au = 0.024 fs, i.e. here we use 0.12 fs)
380.0

….
 Structure of the CPMD input file:
The CPMD section
&CPMD (cont.)
…
TEMPERATURE
300.0
TEMPCONTROL IONS
300.0 40.0 We keep the temperature at 300 ± 40 K
MAXSTEP
10000
TRAJECTORY SAMPLE XYZ
20
STORE
200
…

&END
 Structure of the CPMD input file
SECTIONS
&CPMD

&END

&SYSTEM

&END

&DFT

&END

&ATOMS

&END
 Structure of the CPMD input file:
The SYSTEM section

&SYSTEM
SYMMETRY a2 a3

1 cubic (periodic) box

CELL box enclosing the atoms a1

32.0000 1.0000 1.0000 0.0000 0.0000 0.0000

CUTOFF a1, a2/a1, a3/a1, cos α, cos β, cos γ
70.0 plane wave cutoff
(here cubic box of 32 a.u.**3 )
CHARGE
+0.0 total charge of the system
MULTIPLICITY (M)
3 triplet state (M = 2S+1)
&END
 Structure of the CPMD input file:
The SYSTEM section

&SYSTEM
ANGSTROM
SYMMETRY a2 a3

1 cubic (periodic) box

CELL box enclosing the atoms a1

15.0000 1.0000 1.0000 0.0000 0.0000 0.0000

CUTOFF a1, a2/a1, a3/a1, cos α, cos β, cos γ
70.0 plane wave cutoff
(here cubic box of 15 Å**3 )
CHARGE
0.0 total charge of the system
MULTIPLICITY (M)
3 triplet state (M = 2S+1)
&END
 INSET: BASIS SETS

Atom-centered basis set

Gaussian
function

Plane-wave basis set

Plane
waves
∑ ci (G) exp[iG.r]
ψi (r )=
1
ΩG
Atom-centered basis set

• Give chemical insight

• Depend on atomic position
• Basis set superposition error (BSSE)

Plane-wave basis set

• Less chemical insight
• Independent of atomic position
• No BSSE
∑ ci (G) exp[iG.r] Naturally periodic
ψi (r )=
1 •
ΩG • Many functions needed
• Forces calculation is easier
 &SYSTEM

HOW MANY PLANE WAVES DOES MY SYSTEM NEED?

(i.e. how many basis set functions?)

The number of PWs is defined by Ecutoff and the cell volume

order 3/2 with respect to Ecutoff

1
N PW ≈ 2 Ω E 3/ 2 [a.u.]
cutoff
2π The minimum Ecutoff
Number ot PWs needed depends on
Linear with respect to the cell volume the specific
pseudopotentials
used for each atom
Basis set size:

• Depends on the cell volume

• Does NOT depend on the number of atoms inside the cell

Basic memory depends on Nat, NSP, NPW

≈ (80 + 24 NSP + 4 NAT ) NPW
 &SYSTEM

Working with an isolated cell (not PBC)

… but in QM/MM
method for the solution of the Poisson
&SYSTEM equation for isolated systems ∇2 V (r ) = − 4πρ(r )
H
POISSON TUCKERMAN
SYMMETRY
0 isolated box or cell (also used for QM/MM. I.e. periodic boundary
conditions are not used or the QM region)
CELL
32.0000 1.0000 1.0000 0.0000 0.0000 0.0000
CUTOFF a1, a2/a1, a3/a1, cos α, cos β, cos γ
70.0 plane wave cutoff
(here cubic box of 32 a.u.**3 )
CHARGE
0.0 total charge of the system
MULTIPLICITY
3 a2 a3

&END
a1
Structure of the CPMD input file:
The DFT section

&DFT
FUNCTIONAL HCTH
&END
 Structure of the CPMD input file:
The ATOMS section
&ATOMS
*P_MT_SPR_HCTH.psp
LMAX=D LOC=S Pseudopotential specifications (information on
1 the nonlocality of the pseudopotential).
6.500 6.700 10.000 In general you do not need to change it from
*O_MT_HCTH.psp what is specified in the pseudopotential library
(README file)
LMAX=P LOC=P
2
7.5000 7.000 10.000
6.000 5.000 10.000
*….
CONSTRAINTS
FIX ATOMS
1
23
END CONSTRAINTS
&END
 PSEUDOPOTENTIAL SPECIFICATIONS
./PP_LIBRARY/READ.ME

ELEMENT PP TYPE NAME USAGE REFERENCES

H LDA BHS H_BHS_LDA.psp LMAX=S LOC=S ECUT=25 Ry [1]

H LDA MT (Ballone) H_MT_LDA.psp LMAX=S LOC=S ECUT=25 Ry [2]
H BP MT (Boero) H_MT_BP.psp LMAX=S LOC=S ECUT=25 Ry [15]
H BLYP MT (Boero) H_MT_BLYP.psp LMAX=S LOC=S ECUT=25 Ry [3]
 OUTPUT ENERGIES
NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
1 0.00001 299.6 -545.64887 -473.44754 -473.44754 0.184E-04 18.51
2 0.00010 298.5 -545.37030 -473.44686 -473.44676 0.741E-04 18.25
3 0.00048 296.6 -544.91694 -473.44599 -473.44551 0.173E-03 18.49
4 0.00138 294.1 -544.30697 -473.44522 -473.44384 0.326E-03 18.34
5 0.00301 291.0 -543.56475 -473.44483 -473.44181 0.551E-03 18.43
6 0.00547 287.5 -542.71975 -473.44498 -473.43951 0.866E-03 18.53
7 0.00874 283.7 -541.80538 -473.44575 -473.43701 0.129E-02 18.27
8 0.01273 279.7 -540.85764 -473.44715 -473.43442 0.186E-02 18.43
9 0.01733 275.8 -539.91361 -473.44915 -473.43182 0.258E-02 18.43
10 0.02239 272.0 -539.00979 -473.45151 -473.42912 0.347E-02 20.81

NFI = step number

EKINC = kinetic energy of the fictitious electronic subsystem (in a.u.)
TEMPP = temperature of the system (in K) (i.e. the nuclei)
EKS = Kohn-Sham energy (i.e. the electronic or potential energy)
ECLASSIC = total energy of the nuclei (= EKIN_nuclei + EKS)
EHAM = total energy of the CP system (= ECLASSIC + EKINC)
DIS = mean square displacement of atoms with respect to the first step (in a.u.2)

occ.
EHAM = ECLASSIC +2 ∑ ∫ µ ψ i (r ) 2dr
i
 Structure of the CPMD input file
SECTIONS
&CPMD

&END

&SYSTEM

&END
Other sections:
&DFT & PROPERTIES
& TDDFT
&END & CLASSIC
& VDW
&ATOMS & PIMD
…
&END
 Structure of the CPMD-QMMM input file
In the section &CPMD … &END we simply add the new keyword
QMMM, e.g.
&CPMD
MOLECULAR DYNAMICS
RESTART WAVEFUNCTIONS COORDINATES VELOCITIES LATEST
RESTART ACCUMULATORS LATEST
QMMM
ODIIS
4
…
&END

The sections &DFT … &END, &PROPERTIES … &END, etc..

do not change.
 Structure of the CPMD-QMMM input file
A new section &QMMM … &END must be included
&QMMM
A file that expresses how the force field describes
TOPOLOGY
topology.top
each of the “monomers” of the protein (residues,
COORDINATES ligands …) and their connectivity, the atomic point
coordinates.crd charges etc.
INPUT Name of the file containing the protein coordinates
input.inp
in the appropriate format (gromos format)
AMBER
RCUT_NN
10.
RCUT_MIX force field used (AMBER or GROMOS)
15.
RCUT_ESP
25.
TIMING Gives the time for each part (QM, MM …)
ARRAYSIZES
MAXATT 28
…
&END
 Structure of the CPMD-QMMM input file
A new section &QMMM … &END must be included
&QMMM
TOPOLOGY
topology.top
COORDINATES
coordinates.crd
INPUT
input.inp NN
AMBER
RCUT_NN
10.
RCUT_ESP set the cut-off radii for the 3 regions
25. r1 = 10, r2 = 25
…
&END
QM region
 The 3-regions scheme
NN
Region 1 (“Nearest Neighbor region”):
NN = subset of classical MM atoms inside this region
NN
ρ (x)
∑ qI ∫ d 3 x
I =1 x − RI
r =| x |< r1

Region 2 (“ESP region”):

Classical-RESP charges interaction: QM region

qJRESP ( ρ , R I )
∑ qI ∑
RI − RJ
r1 < r < r2
Note: r1, r2 are taken
I ⸦I ∈
ESP
NN J ∈QM
from any QM atom =>
Region 3 (“MM region”): the regions are not
Multipolar expansion on MM charges: perfectly spherical

℘α ( ρ )(x − R I )
α

∑q ∑
α
∈NN
I
x − RI
3
+ quadrupole r > r2
I ⸦IMM
See Raich et al. Methods Enzymology. 577, 159-183 (2016)
24
for a strategy to chose the radii of the 3 regions
 Structure of the CPMD-QMMM input file

The section &ATOMS … &END looks a bit different

&ATOMS

….

CONSTRAINTS
FIX MM You can fix the whole classical part if you wish
END CONSTRAINTS
&END
 Structure of the CPMD-QMMM input file

The section &ATOMS … &END looks a bit different

&ATOMS
*O_MT_HCTH.psp KLEINMAN-BYLANDER
LMAX=P LOC=P
40
421 435 441 443 444 445 -> give the atom number as listed in
… the coordinates.crd file !
*C_MT_HCTH.psp KLEINMAN-BYLANDER
LMAX=P LOC=P
75
419 422 425 427 429 434 436 438 446 449
…
CONSTRAINTS
FIX MM
END CONSTRAINTS
&END
 OUTPUT ENERGIES IN CPMD
NFI EKINC TEMPP EKS ECLASSIC EHAM DIS TCPU
1 0.00001 299.6 -545.64887 -473.44754 -473.44754 0.184E-04 18.51
2 0.00010 298.5 -545.37030 -473.44686 -473.44676 0.741E-04 18.25
3 0.00048 296.6 -544.91694 -473.44599 -473.44551 0.173E-03 18.49
4 0.00138 294.1 -544.30697 -473.44522 -473.44384 0.326E-03 18.34
5 0.00301 291.0 -543.56475 -473.44483 -473.44181 0.551E-03 18.43
6 0.00547 287.5 -542.71975 -473.44498 -473.43951 0.866E-03 18.53
7 0.00874 283.7 -541.80538 -473.44575 -473.43701 0.129E-02 18.27

NFI = step number

EKINC = kinetic energy of the fictitious electronic subsystem (in a.u.)
TEMPP = temperature of the system (in K) (i.e. the nuclei)
EKS = Kohn-Sham energy (i.e. the electronic or potential energy)
ECLASSIC = total energy of the “classical system” (EKS + EKIN_nuclei)
EHAM = Hamiltonian energy. It is the total energy of the Car-Parrinello system, so
it includes the fictitious kinetic energy of the electrons (EHAM = ECLASSIC + EKINC)
DIS = mean square displacement of atoms with respect to the first step (in a.u.2)
occ.
EHAM = ECLASSIC +2 ∑ ∫ µ ψ i (r ) 2dr
i
 OUTPUT ENERGIES IN CPMD-QMMM
NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU
1 0.00001 299.6 -545.64887 -473.44754 -473.44754 -299.64429 0.184E-04 18.51
2 0.00010 298.5 -545.37030 -473.44686 -473.44676 -299.65252 0.741E-04 18.25
3 0.00048 296.6 -544.91694 -473.44599 -473.44551 -299.66511 0.173E-03 18.49
4 0.00138 294.1 -544.30697 -473.44522 -473.44384 -299.68169 0.326E-03 18.34
5 0.00301 291.0 -543.56475 -473.44483 -473.44181 -299.70173 0.551E-03 18.43
6 0.00547 287.5 -542.71975 -473.44498 -473.43951 -299.72458 0.866E-03 18.53
7 0.00874 283.7 -541.80538 -473.44575 -473.43701 -299.74951 0.129E-02 18.27

NFI = step number

EKINC = kinetic energy of the fictitious electronic subsystem (in a.u.)
TEMPP = temperature of the system (in K) (i.e. the nuclei)
EKS = Kohn-Sham energy (i.e. the electronic or potential energy)
ECLASSIC = total “classical” energy of the system (= EKS + EKIN_nuclei )
EHAM = total energy of the CP system (= ECLASSIC + EKINC)
EQM = energy of the QM region (elecronic + kinetic energy). The QM atoms
are polarized by the MM environment
DIS = mean square displacement of atoms with respect to the first step (in a.u.2)
 OUTPUT ENERGIES IN CPMD-QMMM
NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU
1 0.00001 299.6 -545.64887 -473.44754 -473.44754 -299.64429 0.184E-04 18.51
2 0.00010 298.5 -545.37030 -473.44686 -473.44676 -299.65252 0.741E-04 18.25
3 0.00048 296.6 -544.91694 -473.44599 -473.44551 -299.66511 0.173E-03 18.49
4 0.00138 294.1 -544.30697 -473.44522 -473.44384 -299.68169 0.326E-03 18.34
5 0.00301 291.0 -543.56475 -473.44483 -473.44181 -299.70173 0.551E-03 18.43
6 0.00547 287.5 -542.71975 -473.44498 -473.43951 -299.72458 0.866E-03 18.53
7 0.00874 283.7 -541.80538 -473.44575 -473.43701 -299.74951 0.129E-02 18.27
8 0.01273 279.7 -540.85764 -473.44715 -473.43442 -299.77581 0.186E-02 18.43
9 0.01733 275.8 -539.91361 -473.44915 -473.43182 -299.80291 0.258E-02 18.43
10 0.02239 272.0 -539.00979 -473.45151 -473.42912 -299.83032 0.347E-02 20.81

They refer to the whole system (QM and MM regions)

 OUTPUT ENERGIES IN CPMD-QMMM
NFI EKINC TEMPP EKS ECLASSIC EHAM EQM DIS TCPU
1 0.00001 299.6 -545.64887 -473.44754 -473.44754 -299.64429 0.184E-04 18.51
2 0.00010 298.5 -545.37030 -473.44686 -473.44676 -299.65252 0.741E-04 18.25
3 0.00048 296.6 -544.91694 -473.44599 -473.44551 -299.66511 0.173E-03 18.49
4 0.00138 294.1 -544.30697 -473.44522 -473.44384 -299.68169 0.326E-03 18.34
5 0.00301 291.0 -543.56475 -473.44483 -473.44181 -299.70173 0.551E-03 18.43
6 0.00547 287.5 -542.71975 -473.44498 -473.43951 -299.72458 0.866E-03 18.53
7 0.00874 283.7 -541.80538 -473.44575 -473.43701 -299.74951 0.129E-02 18.27
8 0.01273 279.7 -540.85764 -473.44715 -473.43442 -299.77581 0.186E-02 18.43
9 0.01733 275.8 -539.91361 -473.44915 -473.43182 -299.80291 0.258E-02 18.43
10 0.02239 272.0 -539.00979 -473.45151 -473.42912 -299.83032 0.347E-02 20.81

These energies refer to the QM region

 QM/MM simulation protocol
(http://www.pdb.org) PDB structure

• add H atoms
• choose protonation states system
• add counterions preparation
• solvate
• run MM program (structure relaxation)

Relax structure (classical MD)

• run MM program (MD at constant T/P)

rmsd

Equilibrate structure (classical MD)

• prepare the QM/MM system, choose QM region

• run QM/MM program (structure relaxation)

Relax + equilibrate structure (QM/MM MD)

• run QM/MM dynamics QM/MM trajectory

 Specific for AMBER followed by CPMD QM/MM

Coordinates
1. System preparation Topology

2. Classical MD simulation ./amber_to_gromos

(convertor)

3. Format conversion
Gromos input file
New topology
4. QM/MM simulation New coordinates

cpmd input CPMD

cpmd output files