[gmx-users] Position restraint of crystal waters
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Wed Apr 25 05:18:40 CEST 2012
Hi gmxusers,
Hope you are well. I am trying to apply position restraints to my crystal waters (just briefly, 1-2ns) but have been unsuccessful.
Taking into account the advice from this thread http://lists.gromacs.org/pipermail/gmx-users/2012-February/068780.html, this was what I had done:
system: 1 protein, 13 crystal water,334 POPC, 1 ligand (ZMA), spc solvent , 11 CL
1) EM (steep) then EM (cg) with flexible water
2) NVT with position restraint on all protein heavy atoms, P8 of lipid, ligand, 13 crystal water
in the coordinate file
I have named the waters as CRW
621CRW OW20247 6.056 5.081 7.144
621CRW HW120248 5.961 5.040 7.146
621CRW HW220249 6.098 5.042 7.228
622CRW OW20250 5.191 5.725 8.827
622CRW HW120251 5.244 5.701 8.742
622CRW HW220252 5.193 5.827 8.836
623CRW OW20253 5.726 5.327 7.588
623CRW HW120254 5.673 5.409 7.612
623CRW HW220255 5.666 5.269 7.530
624CRW OW20256 5.815 4.963 7.163
624CRW HW120257 5.755 5.047 7.154
624CRW HW220258 5.759 4.888 7.127
625CRW OW20259 5.657 5.171 7.124
625CRW HW120260 5.640 5.254 7.182
625CRW HW220261 5.586 5.174 7.050
626CRW OW20262 5.960 6.029 6.666
626CRW HW120263 6.046 6.068 6.706
626CRW HW220264 5.981 5.933 6.645
627CRW OW20265 5.037 5.988 6.925
627CRW HW120266 5.045 5.984 6.823
627CRW HW220267 5.028 5.891 6.956
628CRW OW20268 5.902 6.305 7.209
628CRW HW120269 5.841 6.300 7.125
628CRW HW220270 5.983 6.357 7.179
629CRW OW20271 5.649 5.829 8.592
629CRW HW120272 5.641 5.726 8.595
629CRW HW220273 5.572 5.859 8.533
630CRW OW20274 5.638 5.631 8.294
630CRW HW120275 5.633 5.598 8.390
630CRW HW220276 5.542 5.639 8.264
631CRW OW20277 5.191 4.965 7.665
631CRW HW120278 5.133 4.996 7.585
631CRW HW220279 5.272 4.922 7.621
632CRW OW20280 5.633 5.385 7.286
632CRW HW120281 5.595 5.459 7.343
632CRW HW220282 5.734 5.383 7.307
633CRW OW20283 5.888 5.393 7.368
633CRW HW120284 5.984 5.363 7.354
633CRW HW220285 5.860 5.364 7.462
in the .top file
; Include forcefield parameters
#include "gromos53a6_lipid.ff/forcefield.itp"
;Include Protein Topology
#include "A1.itp"
#ifdef STRONG_POSRES
#include "strong_posre.itp"
#endif
;
#ifdef POSRES
#include "posre.itp"
#endif
;Include POPC topology
#include "popc.itp"
#ifdef LIPID_POSRES
#include "lipid_posre.itp"
#endif
;
;Include ZMA topology
#include "mod_zma.itp"
#ifdef ZMA_POSRES
#include "zma_posre.itp"
#endif
;Include crystal water topology
#include "gromos53a6_lipid.ff/crw.itp"
#ifdef CRW_POSRES
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
;
;Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "gromos53a6_lipid.ff/ions.itp"
[ system ]
; Name
PROTEIN POP ZMA CRW SOL
[ molecules ]
; Compound #mols
Protein_chain_X 1
POPC 334
ZMA 1
CRW 13
SOL 31491
CL 11
in crw.itp
[ moleculetype ]
; molname nrexcl
CRW 2
[ atoms ]
; nr type resnr residue atom cgnr charge mass
#ifndef HEAVY_H
1 OW 1 CRW OW 1 -0.82 15.99940
2 H 1 CRW HW1 1 0.41 1.00800
3 H 1 CRW HW2 1 0.41 1.00800
#else
1 OW 1 CRW OW 1 -0.82 9.95140
2 H 1 CRW HW1 1 0.41 4.03200
3 H 1 CRW HW2 1 0.41 4.03200
#endif
in NVT.mdp
title = NVT equilibration
define = -DPOSRES -DLIPID_POSRES -DZMA_POSRES -DCRW_POSRES
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 100000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 5000 ; save coordinates every 10 ps
nstvout = 5000 ; save velocities every 10 ps
nstenergy = 5000 ; save energies every 10 ps
nstlog = 5000 ; update log file every 10 ps
nstxtcout = 5000
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_ZMA POPC SOL_CRW_CL ; three coupling groups - more accurate
tau_t = 0.1 0.1 0.1 ; time constant, in ps
ref_t = 310 310 310 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 310 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
; COM motion removal
; These options remove motion of the protein/bilayer relative to the solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_ZMA_POPC SOL_CRW_CL
when I tried to run NVT, the process crashed at step 10
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
When I changed all CRW to SOL, there was no problem with NVT and subsequent NPT equilibration. The downside is that I could not position restrain the crystal water to prevent any possible initial clashes.
Would really appreciate some help. Thank you in advance!
Huiwen
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