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
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