Pressure should fluctuate significantly. The estimator for the pressure that is generally used is very noisy. The question is, do the pressure averages over, say, 500 ps or 1 ns look about right?
On Sun, Aug 25, 2013 at 5:07 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > On Sun, Aug 25, 2013 at 6:22 PM, rahul seth > <rahul.seth.grom...@gmail.com> wrote: >> Hi All, >> >> I have been trying to perform NPT-REMD with a Protein Substrate and water. >> I am trying to use md+nose-hoover thermostat and parrinello-rahman >> barostat. However, I am not quite sure about the tau-t and the tau-p that I >> should be using here. I paste a part of my mdp file below: >> define = -DPOSRES_subs >> constraints = all-bonds >> pbc = xyz >> integrator = md >> ;ld_seed = %8i >> dt = 0.002 ; ps ! >> nsteps = 250000 ; 50 ns >> ; >> nstcomm = 1 >> nstcalcenergy = 10 >> nstxout = 0 >> nstxtcout = 5000 ;every 10 ps >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 1000 >> nstlist = 10 >> ns_type = grid >> rlist = 1.0 >> vdwtype = cut-off >> rvdw = 1.0 >> coulombtype = pme >> rcoulomb = 1.0 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> optimize_fft = yes >> tcoupl = nose-hoover >> nsttcouple = 5 >> tc-grps = subs Protein SOL >> tau_t = 0.2 0.2 0.2 >> ref_t = %8.3f %8.3f %8.3f >> ; Energy monitoring >> energygrps = subs Protein SOL >> ; Isotropic pressure coupling is now on >> Pcoupl = parrinello-rahman >> nstpcouple = 1 >> refcoord-scaling = all >> Pcoupltype = isotropic >> tau_p = 2.0 >> compressibility = 4.5e-5 >> ref_p = 1.01325 >> >> >> Although the temperatures in this case stays close to the desired values, >> the pressures of the individual replicas fluctuate significantly and hence >> I do not think I have weird replica exchange probabilities. > > Seemingly large > http://www.gromacs.org/Documentation/Terminology/Pressure fluctuations > are normal - see link. You should satisfy yourself that your .mdp file > produces ensembles that are respectable before you get involved with > REMD, and gathering statistics for that will take longer for pressure > than temperature. > >> I have varied tau-t and tau-p from 0.2 to 1 and 1 to 5 respectively. It >> doesn't really seem to improve anything. Can anyone suggest a set of >> optimized values for these parameters? I understand these maybe context >> dependent but to give you a rough idea I have about ~18,000 atoms with 170 >> for atoms 1156 for substrate and the rest for water. > > Your literature survey of similar simulations should give you an idea > of usage in the field, but (e.g. per GROMACS manual thermostat > section) I would think tau-t for N-H should not go below 1. Otherwise, > first observe whether you have a real problem before making haphazard > changes :-) > > Mark > >> -- >> 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 -- 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