[CPMD-list] how to include water in QM part in a QMMM calculation
Yong Zhang
zhangymall11 at gmail.com
Wed May 16 15:16:22 CEST 2007
What is the difference between 999 and -999? When would those be used?
Thanks.
Here is the cpmd input:
=================
&CPMD
MOLECULAR DYNAMICS CP
RESTART COORDINATES VELOCITIES LATEST
QMMM
QUENCH BO
TEMPCONTROL IONS
300.0 50.0
MAXSTEP
10
TIMESTEP
4.0
EMASS
500.
TRAJECTORY SAMPLE XYZ DCD
1
DIPOLE DYNAMICS SAMPLE WANNIER
1
WANNIER REFERENCE
0.0 0.0 0.0
WANNIER SERIAL
&END
&DFT
NEWCODE
FUNCTIONAL PBE
&END
&QMMM
VERBOSE
GROMOS
WRITE LOCALTEMP
SPLIT
TOPOLOGY
nma-79-top.dat
COORDINATES
nma-crd5.dat
INPUT
gromos.inp
UPDATE LIST
20
LONG RANGE ELECTROSTATIC COUPLING
RCUT_NN
10.0
RCUT_MIX
15.0
RCUT_ESP
20.0
ARRAYSIZES
MAXATT 43
MAXAA2 80
MAXNRP 249
MAXNBT 50
MAXBNH 250
MAXBON 66
MAXTTY 50
MXQHEH 189
MAXTH 86
MAXQTY 10
MAXHIH 10
MAXQHI 10
MAXPTY 31
MXPHIH 296
MAXPHI 168
MAXCAG 100
MAXAEX 20390
MXEX14 373
MAXCON 244
END ARRAYSIZES
&END
&SYSTEM
SYMMETRY
0
POISSON SOLVER TUCKERMAN
CELL
12.00 1.0 1.0 0.0 0.0 0.0
CUTOFF
85.0
&END
&ATOMS
*C_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
3
1 5 9
*N_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
1
7
*O_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=P
2
6 223
*H_MT_PBE.psp KLEINMAN-BYLANDER
LMAX=S
9
2 3 4 8 10 11 12 224 225
&END
====================
and this is gromos input:
======================
TITLE
input generated by amber2gromos
END
SYSTEM
# NPM >= 0 number of (identical) solute molecules
# NSM >= 0 number of (identical) solvent molecules
# NPM NSM
1 429
END
START
# NTX 1..3 reading/generation of initial 3D coordinates (X),
# 3D velocities (V), and stochastic integrals (SX)
# action 1 2 3
# read X from IOXVI (21) yes yes yes
# set V to zero if TEMPI = 0.0 yes no no
# read V from IOXVI (21) if TEMPI = 0.0 no yes yes
# read SX from IOXVI (21) no no yes
#
# INIT 1..4 startup configuration
# action 1 2 3 4
# shake X yes no no no
# shake V yes yes no no
# C.O.M removal yes yes yes no
# if NTCM =1
# NTX INIT IG TEMPI HEAT NTXO BOLTZ
1 4 210185 300.0 0.00000 1 0.83144E-02
END
STEP
# NSTLIM > 0 total number of steps
# T >= 0.0 time at beginning of simulation
# DT >= 0.0 time step of simulations
# NSTLIM T DT
10 0.00 0.00200
END
BOUNDARY
# NTB -2..2 define boundary conditions
# <0 truncated octahedron periodic boundary conditions
# >0 rectangular/monoclinic periodic boundary conditions
# 0 vacuum
# abs(NTB) = 2 the virial (pressure) is calculated
# BOX(1..3) > 0.0 periodic box dimensions
# BETA > 0.0 angle of box (inclination between x- and z-axes) in degrees
# BETA must be 90.0 degrees if abs(NTB) = 2 or if NTB<0
# NRDBOX 0,1 controls reading of BOX dimensions
# 0 use the box dimensions from the BOUNDARY block
# 1 read box dimensions from startup file (BOX) IOXVI
# NTB BOX(1) BOX(2) BOX(3) BETA NRDBOX
1 2.501000000 2.501000000 2.501000000 90.00 0
END
SUBMOLECULES
# NSPM > 0 number of (sub)molecules the solute consists of
# NSP(1.. NSPM) > 0 atom sequence number in topology
# of last atom in submolecule I
# NSPM NSP(1.. NSPM)
80 12 15 18 21 24 27 30 33 36 39 42
45 48 51 54 57 60 63 66 69 72 75 78 81 84
87 90 93 96 99 102 105 108 111 114 117 120
123 126 129 132 135 138 141 144 147 150 153 156
159 162 165 168 171 174 177 180 183 186 189
192 195 198 201 204 207 210 213 216 219 222
225 228 231 234 237 240 243 246 249
END
TCOUPLE
# NTT(1) -3..3 controls temperature coupling of solute
# internal and rotational degrees of freedom ( d.o.f.) in three dimensions
# NTT(2) -3..3 controls temperature coupling of solute
# centre of mass translational d.o.f. in three dimensions
# NTT(3) -3..3 controls temperature coupling of solvent d.o.f.
# in three dimensions
# 0 no temperature coupling for set of d.o.f.
# 1 couple one set of d.o.f. to one bath
# 2,-2 couple two sets of d.o.f. to one bath (+ sign)
# -3,3 couple three sets of d.o.f. to one bath (+ sign)
# TEMP0 >= 0.0 bath reference temperature
# TAUT >= 0.0 coupling time
# NTT TEMP0 TAUT
0 300.0 0.100
0 300.0 0.100
0 300.0 0.100
END
CENTREOFMASS
# NDFMIN >= 0 number of degrees of freedom to subtract from total
# when calculating the system temperature
# NTCM 0,1 controls initial centre of mass motion removal
# 0 no initial centre of mass motion removal
# 1 inital centre of mass motion is removed
# NSCM >= 0 controls centre of mass motion removal during
# simulation
# 0 no centre of mass motion removal
# > 0 centre of mass motion removal every NSCM steps
# NDFMIN NTCM NSCM
0 0 100000
END
PRINT
# NTPR: print out energies, etc. every NTPR steps
# NTPL: print out C.O.M motion and total energy fitting every NTPL steps
# NTPP: =1 perform dihedral angle transition monitoring
# NTPR NTPL NTPP
1 100 0
END
WRITE
# NTPW = 0 : binary
# NTPW = 1 : formatted
# NTWSE = configuration selection parameter
# =0: write normal trajectory
# >0: chose min energy for writing configurations
# NTWX NTWSE NTWV NTWE NTWG NTPW
1 0 1 1 0 1
END
SHAKE
# NTC 1,2,3 controls use of SHAKE for the solute
# 1 no shake is performed (solute)
# 2 SHAKE the bonds involving hydrogens (solute)
# 3 SHAKE all bonds (solute)
# TOL > 0.0 SHAKE tolerance (relative geometric
# precision), for solute and solvent
# NTC TOL
1 0.0000010
END
FORCE
# NTF(I)=0 do not use term I
# NTF(I)=1 use term I
# NTF(1) bonds involving hydrogens
# NTF(2) bonds not involving hydrogens
# NTF(3) bond angles involving hydrogens
# NTF(4) bond angles not involving hydrogens
# NTF(5) improper dihedrals involving hydrogens
# NTF(6) improper dihedrals not involving hydrogens
# NTF(7) dihedrals involving hydrogens
# NTF(8) dihedrals not involving hydrogens
# NTF(9) nonbonded charge interactions
# NTF(10) nonbonded interactions
# NEGR >= 0 number of energy groups
# NRE > 0 last atoms in each energy group
# NRE values must be in ascending order
# bonds angles imp. dihe charge nonbonded
# H H H H
1 1 1 1 1 1 1 1 1 1
# NEGR NRE(1) NRE(2) ... NRE(NEGR)
2 249 1536
END
PLIST
# NTNB 0,1 controls pairlist construction before the first step
# 0 no pairlist is constructed before the first step
# 1 a pairlist is constructed before the first step
# NSNB > 0 controls frequency (number of steps) a pairlist is
# constructed
# RCUTP > 0.0 cut-off used in pairlist construction
# RCUTL > 0.0 cut-off used in long range interaction
# NTNB NSNB RCUTP RCUTL
1 10 0.80 1.00
END
LONGRANGE
# EPSRF =0.0,or >= 1.0 eps used in reaction-field calc.
# APPAK >= 0.0 kappa used in reaction-field calc.
# RCRF > 0.0 cut-off radius used in reaction-field calc.
# EPSRF APPAK RCRF
54.0 0.0 1.00
END
LATSUM
# 32 is the ewald grid, 64 is a more conservative choice
# 0.7 is the size of the head function for ewald summation
2 64 64 64 0 0.80000 1.33000 100000
END
POSREST
# values for NTR
# 0: no position re(con)straining
# 1: use CHO
# 2: use CHO/ ATOMIC B-FACTORS
# 3: position constraining
# NTR CHO NRDRX
0 1000 0
END
=====================
On 5/16/07, Paul Fleurat-Lessard <Paul.Fleurat-Lessard at ens-lyon.fr> wrote:
>
> Hi,
>
> Can you send us your input file ? It might be that you impose a
> constraint with 999. instead of -999.
>
> Regards,
> Paul.
>
> Yong Zhang a écrit :
> > Hi CPMDers,
> >
> > I am setting up a QMMM calculation using cpmd/gromos. I want to include
> > a small peptide and several water molecules in the QM part. When I first
> > tried QM=peptide, it is working fine. But when I can added H2O into QM,
> > I got a error:
> >
> > ###########
> >
> > ================================================================
> > == END OF FORCES INITIALIZATION ==
> > ================================================================
> >
> > CPU TIME FOR INITIALIZATION: 121.27 SECONDS
> > MM_DIM| called with: mm_go_mm
> > MM_DIM| old status : MM
> > MM_DIM| new status : MM
> > ***MM_SOLV_CO| SIZE OF THE PROGRAM IS 156032/ 439876 kBYTES ***
> > -48.4249572386251 0.274943057696344 6.66473917142948
> > 1.53747889055130 -3.42658725556664 2.66146148402518
> > -16.9038987425283
> >
> >
> > PROGRAM STOPS IN SUBROUTINE SHAKE_SM| CONSTRAINT FAILURE
> > 999
> > ##############
> >
> > The water is part of solute (residue H2O). It is weird because no shake
> > or constraint is used in either cpmd input or gromos input. Anybody has
> > met the same problem? Is this related to the SPC water model? How to
> > overcome this problem? Thanks a lot.
> >
> > best wishes,
> >
> > Yong
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > CPMD-list mailing list
> > CPMD-list at cpmd.org
> > http://cpmd.org/mailman/listinfo/cpmd-list
>
> --
> Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard at ens-lyon.fr
> Laboratoire de Chimie
> Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54
> 46, Allée d'Italie Fax: + 33 (0)4 72 72 88 60
> 69364 Lyon Cedex 07
>
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