Hi Justin, okey then I will try it with this timestep. No it is not my goal to do a NVE. I already had temperature coupling options in my .mdp file but on the blowing up side was written "you are using inappropriate temperature coupling" so I thought that that might be the reason and deleted it from my .mdp file.
I had the following temperature coupling options: tcoupl = V-rescale tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 298 298 pcoupl = no Thank you for your answer. Eva > > > On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi everybody, >> I want to do a md for a protein with a membrane around it. >> I already minimised the energy of the protein. >> >> >> >> Output of the minimization: >> >> ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, >> atom= 1653 >> Stepsize too small, or no change in energy. >> Converged to machine precision, >> but not to the requested precision Fmax < 10 >> >> Double precision normally gives you higher accuracy. >> You might need to increase your constraint accuracy, or turn >> off constraints alltogether (set constraints = none in mdp file) >> >> writing lowest energy coordinates. >> >> >> Steepest Descents converged to machine precision in 813 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.5928356e+05 >> Maximum force = 3.6197971e+02 on atom 1653 >> Norm of force = 2.6517429e+00 >> >> >> >> >> >> In my eyes this output was okey so I went on with the md. >> And here I get the error: >> >> Fatal error: >> A charge group moved too far between two domain decomposition steps >> This usually means that your system is not well equilibrated >> >> >> >> >> I already read the error page for this error and also the blowing up >> page >> but I still do not know what to do now. >> >> My .mdp file for the md runs looks like this: >> >> define = -DPOSRES >> integrator = md >> dt = 0.005 > > This timestep is huge. Even with constraints, you probably can't exceed 2 > fs > stably (0.002 ps). > >> nsteps = 2000 >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstxtcout = 0 >> nstenergy = 5 >> energygrps = Protein Non-Protein >> nstcalcenergy = 5 >> nstlist = 10 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> gen_vel = yes >> gen_temp = 200.0 >> gen_seed = 9999 >> constraints = all-bonds >> >> >> Are here any optinos which can cause the error? >> > > In the absence of temperature and/or pressure coupling, the ensemble > you're > trying to simulate is NVE, which is very tricky to get stabilized. > > http://www.gromacs.org/Documentation/Terminology/NVE > > If you're not going for an NVE ensemble, you need several adjustments in > the > .mdp file. See any basic tutorial for examples of how to simulate other > ensembles, if this is your goal. > > -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 > * Only plain text messages are allowed! > * 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? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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? Read http://www.gromacs.org/Support/Mailing_Lists
