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. 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. -- 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
