I also noticed this error on my setup, so I changed tau-t to 0.1, which is commonly found on others setup. tau-t = 0.0109 seems too low.
2010/11/26 Per Larsson <per.lars...@sbc.su.se> > 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 >
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