Try to use constrains = all-bonds which is the way to use Gromos force fields.
On Mar 26, 2012, at 12:30, SebastianWaltz <sebastian.wa...@physik.uni-freiburg.de> wrote: > Dear Gromacs user, > > I try to simulate the human Villin head peace HP35 in approx. 6000 water > molecules (spc) with the gromos ff ffG53a6. Using the 4.0.7 version the > NPT equilibration for 5ns with position restraint protein (lincs) atoms > and a integration step of 0.002 using the leap-frog integrator works > just fine. Switching to the 4.5.5 or the 4.6 version with heterogeneous > acceleration is leading to an exploding protein after a few ps. Changing > the integration time step to 0.0002 delays the explosion for few ps but > does not avoid it. The parameters in mdp file for the 4.6 version are > the following: > > ; > title = ttt > cpp = /lib/cpp > include = -I../top > constraints = hbonds > integrator = md > cutoff-scheme = verlet > > define = -DPOSRES > ;constraint_algorithm = shake > dt = 0.0002 > nsteps = 2500000 > nstcomm = 10 > nstxout = 1000 > nstvout = 1000 > nstfout = 1000 > nstlog = 1000 > nstenergy = 5000 > nstxtcout = 10 > > xtc_grps = Protein > > nstlist = 25 > ns_type = grid > rlist = 1.2 > > coulombtype = PME > rcoulomb = 1.2 > vdwtype = cut-off > rvdw = 1.2 > fourierspacing = 0.12 > pme_order = 6 > optimize_fft = yes > pbc = xyz > Tcoupl = v-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 300 300 > > energygrps = Protein Non-Protein > > Pcoupl = berendsen > tau_p = 0.5 > compressibility = 4.5e-5 > ref_p = 1.0 > refcoord_scaling = all > Pcoupltype = isotropic > gen_vel = yes > gen_temp = 300 > gen_seed = -1 > > > Any help is very welcomed. > > Dears sincerely, > > Sebastian > -- > 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 -- 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
