Dear Grzegorz: >From a quick look at your .mdp, I also suggest that you go back to your system >including the peptide that you had managed to finish EM with modified flexible >tip5p but then crashed with the standard rigid tip5p during MD and try the MD >again using gen-vel = yes
if you're still seeing problems, why not upload your water-only system and your with-small-peptide test system to redmine. It's meant as a place to start a discussion, share files, and help us not to foget about a problem that may exist, so I am not sure why you hesitate. Also, you said that the authors of that other OPLS-Tip5p paper had no problems. You might ask them for .gro .mdp and .top files so that you can see exactly what they did and how it differs from what you are doing. Chris. -- original message -- P.s. The mdp: constraints = none integrator = md dt = 0.001 ; ps nsteps = 10000000 ; total 10 ns nstcomm = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstxtcout = 25 xtc_grps = System nstlog = 1000 nstenergy = 1000 nstlist = 20 ns_type = grid rlist = 1.3 coulombtype = PME fourierspacing = 0.1 pme_order = 4 optimize_fft = yes rcoulomb = 1.3 rvdw = 1.3 vdwtype = cut-off pbc = xyz DispCorr = EnerPres Tcoupl = v-rescale ld_seed = -1 tc-grps = System tau_t = 0.1 ref_t = 300.0 pcoupl = Parrinello-Rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = no cutoff-scheme = Verlet -- 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? Read http://www.gromacs.org/Support/Mailing_Lists
