Dear all, <br>I am trying to set up a REMD simulation for a peptide (CHARMM ff) in implicit solvent (OBC GB). <br>Following Bjelkmar et al* I am using stochastics dynamics integration with an inverse friction constant of 91 ps-1, 5 fs timestep, <br>
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 <br>facing is that after a while, the temperatures of all replicas start dropping even below the lowest target temperature. <br>
Would you suggest changing some parameter or the whole thermostat to prevent this from happening?<br><br>@ s0 legend "Temperature"<br> 0.000000 310.811523<br> 5.000000 435.627045<br> 10.000000 417.161713<br>
15.000000 414.248901<br> 20.000000 399.390686<br> 25.000000 375.087219<br> 30.000000 338.131256<br> 35.000000 339.961151<br> 40.000000 319.424561<br> 45.000000 290.442322<br> 50.000000 289.587921<br>
55.000000 248.746246<br> 60.000000 253.192047<br> 65.000000 242.619476<br> 70.000000 256.051941<br> 75.000000 237.648468<br> 80.000000 231.938690<br> 85.000000 217.029953<br> 90.000000 211.447983<br>
95.000000 210.393890<br> 100.000000 208.518417<br> 105.000000 196.718445<br> 110.000000 219.245682<br> 115.000000 202.957993<br> 120.000000 193.128159<br> 125.000000 198.278198<br> 130.000000 175.304108<br>
135.000000 164.925613<br> 140.000000 195.024490<br> 145.000000 201.153046<br> 150.000000 211.160797<br> 155.000000 189.525085<br> 160.000000 191.156006<br> 165.000000 186.545242<br> 170.000000 186.885422<br>
175.000000 182.838486<br> 180.000000 174.960098<br> 185.000000 175.244049<br> 190.000000 179.517975<br> 195.000000 165.785416<br> 200.000000 189.871048<br> 205.000000 179.510178<br> 210.000000 152.527710<br>
215.000000 160.109955<br> 220.000000 163.564148<br><br><br><br><br><br><br><br><br><br>* "Implementation of the CHARMM ff in GROMACS" (2010) JCTC, 6, 459-466<br><br><br>; Run parameters<br>integrator = sd<br>
dt = 0.005 ; ps ! <br>nsteps = 20000<br>nstcomm = 1<br>comm_mode = angular ; non-periodic system<br><br>; Bond parameters<br>constraints = all-bonds<br>
constraint_algorithm = lincs<br>lincs-iter = 1<br>lincs-order = 6<br><br>; required cutoffs for implicit<br>nstlist = 0 <br>ns_type = grid<br>rlist = 0 <br>rcoulomb = 0 <br>
rvdw = 0 <br>epsilon_rf = 0<br>rgbradii = 0<br><br>; cutoffs required for qq and vdw<br>coulombtype = cut-off<br>vdwtype = cut-off<br><br>; temperature coupling<br>
tcoupl = v-rescale<br>tc-grps = system<br>tau-t = 91<br>ref-t = 300<br><br>; Pressure coupling is off<br>Pcoupl = no<br><br>; Periodic boundary conditions are off for implicit<br>
pbc = no<br><br>; Settings for implicit solvent<br>implicit_solvent = GBSA<br>gb_algorithm = OBC<br>gb_epsilon_solvent = 78.3<br>sa_surface_tension = 2.25936<br><br>;Output control<br>nstxout = 1000<br>
nstfout = 0<br>nstvout = 0<br>nstxtcout = 0<br>nstlog = 1000<br>nstcalcenergy = -1<br>nstenergy = 1000<br><br>; GENERATE VELOCITIES FOR STARTUP RUN<br>gen_vel = yes<br>
gen_temp = 300<br>gen_seed = 1993<br><br><br><br>