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 << This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK & Malaysia legislation. >>
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