Thanks for your reply. I' d like to know if I need to remove all position restraints before MDRUN?means that the last step of npt should be done without position restraints?
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, April 19, 2013 7:58 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:26 AM, Shima Arasteh wrote: > Hi, > > I tried to equilibrate my system by setting timestep=1 fts and decreasing the > position restraints step by step. > > But when I go to MDRUN step, it doesnt work and some pdb files are printed. > > what is printed in my log file is as follow: > > Step Time Lambda > 0 0.00000 0.00000 > > Energies (kJ/mol) > U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 > 8.34161e+04 5.57602e+04 7.65365e+02 -1.97155e+02 8.52248e+03 > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > -1.06644e+05 8.46716e+04 -5.77343e+03 -1.11612e+06 -2.67240e+05 > Potential Kinetic En. Total Energy Temperature Pres. DC (bar) > -1.26284e+06 6.13687e+05 -6.49154e+05 8.17667e+02 -1.08370e+02 > Pressure (bar) Constr. rmsd > -8.62031e+04 5.99322e-04 > > > > Would you please give me any suggestions? Does my system need more > equilibration yet? longer equilibration time? > Whats the problem? My settings as sent you earlier seem fine, so whats the > solution? > > Thanks for your suggestions. They would be appreciated. > The temperature is 817 K, indicating something is moving with a ridiculously high velocity that has been imparted by strong forces. You have atoms overlapping somewhere. Try more thorough energy minimization. -Justin > > > Sincerely, > Shima > > > ________________________________ > From: Justin Lemkul <jalem...@vt.edu> > To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS > users <gmx-users@gromacs.org> > Sent: Sunday, April 7, 2013 4:46 PM > Subject: Re: [gmx-users] unstable system > > > > > > > > > On Sun, Apr 7, 2013 at 1:41 AM, Shima Arasteh <shima_arasteh2...@yahoo.com> > wrote: > > Hi all, >> >> I have a system of peptide/POPC/water/ions. The energy minimization and >>NVT steps has passed successfully. I ran NPT step for around 10 ns with >>restraints of protein and P atoms at first nano seconds and then removing >>them gradually. >> I tried to go on MDRUN. I did not remove restraint of protein atoms >> completely and they are still restrained. When I run the mdrun command, I >> get error of "X particles communicated to PME node Y are more than a cell >> length out of the domain decomposition cell of their charge group" . >> I know this error means an unstable system. When I visualized the written >> pdb files, I see some popc hydrogen atoms are broken and located between two >> leaflets which are separated by a gap. The protein seems ok, however I >> don't get many pdb files to see. >> >> >> As what I see in Diagnosing unstable system web page, >> 1. it would be beneficial if one see what part of the system is unstable in >> first steps. As I saw, the unstable "POPC hydrogen atoms" are not fine. >> 2. The single molecules are supposed to examine in water or vacuum too. I >> have passed this step successfully. >> 3. I have not ignored any warning during the last steps. >> 4. And my mdp files to run md is as follow: >> >> integrator = md >> dt = 0.002 >> nsteps = 5000000 >> >> >> ns_type = grid >> nstlist = 5 >> rlist = 1.2 >> rlistlong = 1.4 >> rcoulomb = 1.2 >> rvdw = 1.2 >> pbc = xyz >> vdwtype = switch >> rvdw_switch = 1.0 >> > > What force field are you using? CHARMM? In any case, the value of rvdw_switch > does not make any sense. If you're using CHARMM, it should be 1.0. > > ; Parameters for treating bonded interactions >> continuation = yes >> constraint_algorithm = LINCS NCS / SHAKE) >> constraints = all-bonds ) >> lincs_iter = 1 >> lincs_order = 4 >> >> ; Parameters for treating electrostatic interactions >> coulombtype = PME ; Long range electrostatic interactions >> treatment (cut-off, Ewald, PME) >> pme_order = 4 ; Interpolation order for PME (cubic interpolation >> is represented by 4) >> fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using >> PME (nm) >> >> ; Temperature coupling parameters >> tcoupl = Nose-Hoover >> tc-grps = Protein_POPC Water_and_ions ; Define groups to be >> coupled separately to temperature bath >> tau_t = 0.5 0.5 ; Group-wise coupling time constant >> (ps) >> ref_t = 310 310 ; Group-wise reference temperature (K) >> >> ; Pressure coupling parameters >> pcoupl = Parrinello-Rahman >> pcoupltype = semiisotropic >> tau_p = 2.0 >> ref_p = 1.01325 1.01325 >> compressibility = 4.5e-5 4.5e-5 >> >> ; Miscellaneous control parameters >> ; Dispersion correction >> DispCorr = EnerPres >> ; Initial Velocity Generation >> gen_vel = no >> ; Centre of mass (COM) motion removal relative to the specified groups >> nstcomm = 1 y (steps) >> comm_mode = Linear >> comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the >> specified groups >> >> Would you please let me know if these happen due to an improper >>equilibration? Do I need to extend the NPT step? Would that fix it? >> >> > > Aside from the above comment, there is nothing particularly wrong about the > .mdp file aside from some odd characters here and there, which I will assume > are nothing more than quirks of transferring to an email, as they otherwise > would have triggered fatal errors in grompp. > > -Justin > -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? 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