All right. And if minimization doesnt fix such a problem, what would be the solution? However I have not tried it on my own system yet.
Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Friday, April 19, 2013 8:22 PM Subject: Re: [gmx-users] unstable system On 4/19/13 11:43 AM, Shima Arasteh wrote: > 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? > Whatever makes sense for your system. There is no universal answer to how equilibration should be done. If your simulation is crashing at step zero, I doubt that removing restraints will help in any way. -Justin > > > 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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