Hi! Have never tried remd with implicit solvent, but note that the unit of tau-t in the mdp-file is ps, not ps-1. This means you should set tau-t = 0.0109 rather than 91.
Try this and see if the problem goes away! /Per 26 nov 2010 kl. 15:55 skrev César Ávila <clav...@gmail.com>: > Dear all, > I am trying to set up a REMD simulation for a peptide (CHARMM ff) in implicit > solvent (OBC GB). > Following Bjelkmar et al* I am using stochastics dynamics integration with an > inverse friction constant of 91 ps-1, 5 fs timestep, > virtual-sites for hydrogens, all-vs-all nonbonded (no cutoff). The full .mdp > file is attached at the end of this mail. The problem I am > facing is that after a while, the temperatures of all replicas start dropping > even below the lowest target temperature. > Would you suggest changing some parameter or the whole thermostat to prevent > this from happening? > > @ s0 legend "Temperature" > 0.000000 310.811523 > 5.000000 435.627045 > 10.000000 417.161713 > 15.000000 414.248901 > 20.000000 399.390686 > 25.000000 375.087219 > 30.000000 338.131256 > 35.000000 339.961151 > 40.000000 319.424561 > 45.000000 290.442322 > 50.000000 289.587921 > 55.000000 248.746246 > 60.000000 253.192047 > 65.000000 242.619476 > 70.000000 256.051941 > 75.000000 237.648468 > 80.000000 231.938690 > 85.000000 217.029953 > 90.000000 211.447983 > 95.000000 210.393890 > 100.000000 208.518417 > 105.000000 196.718445 > 110.000000 219.245682 > 115.000000 202.957993 > 120.000000 193.128159 > 125.000000 198.278198 > 130.000000 175.304108 > 135.000000 164.925613 > 140.000000 195.024490 > 145.000000 201.153046 > 150.000000 211.160797 > 155.000000 189.525085 > 160.000000 191.156006 > 165.000000 186.545242 > 170.000000 186.885422 > 175.000000 182.838486 > 180.000000 174.960098 > 185.000000 175.244049 > 190.000000 179.517975 > 195.000000 165.785416 > 200.000000 189.871048 > 205.000000 179.510178 > 210.000000 152.527710 > 215.000000 160.109955 > 220.000000 163.564148 > > > > > > > > > > * "Implementation of the CHARMM ff in GROMACS" (2010) JCTC, 6, 459-466 > > > ; Run parameters > integrator = sd > dt = 0.005 ; ps ! > nsteps = 20000 > nstcomm = 1 > comm_mode = angular ; non-periodic system > > ; Bond parameters > constraints = all-bonds > constraint_algorithm = lincs > lincs-iter = 1 > lincs-order = 6 > > ; required cutoffs for implicit > nstlist = 0 > ns_type = grid > rlist = 0 > rcoulomb = 0 > rvdw = 0 > epsilon_rf = 0 > rgbradii = 0 > > ; cutoffs required for qq and vdw > coulombtype = cut-off > vdwtype = cut-off > > ; temperature coupling > tcoupl = v-rescale > tc-grps = system > tau-t = 91 > ref-t = 300 > > ; Pressure coupling is off > Pcoupl = no > > ; Periodic boundary conditions are off for implicit > pbc = no > > ; Settings for implicit solvent > implicit_solvent = GBSA > gb_algorithm = OBC > gb_epsilon_solvent = 78.3 > sa_surface_tension = 2.25936 > > ;Output control > nstxout = 1000 > nstfout = 0 > nstvout = 0 > nstxtcout = 0 > nstlog = 1000 > nstcalcenergy = -1 > nstenergy = 1000 > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp = 300 > gen_seed = 1993 > > > > -- > 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
