I also noticed this error on my setup, so I changed tau-t to 0.1, which is commonly found on others setup.<br>tau-t = 0.0109 seems too low.<br><br><div class="gmail_quote">2010/11/26 Per Larsson <span dir="ltr"><<a href="mailto:per.larsson@sbc.su.se">per.larsson@sbc.su.se</a>></span><br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">Hi!<br>
<br>
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.<br>
<br>
Try this and see if the problem goes away!<br>
<br>
/Per<br>
<br>
26 nov 2010 kl. 15:55 skrev César Ávila <<a href="mailto:clavila@gmail.com">clavila@gmail.com</a>>:<br>
<div><div></div><div class="h5"><br>
> 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>
</div></div>> --<br>
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