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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
