Thank you for the discussion. I am basically having a similar problem: position restraining (PR) 2 plates in NPT and the system blow up (posted here: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055975.html). I will try to use smaller time step to see whether the situation becomes better. A quick question, can we really do meaningful NPT simulation with PR, in which the position need to be almost like fixed? I know we cannot do freeze. PR supposed to be OK, right?
Thanks, Zhe On Sun, Nov 21, 2010 at 9:51 AM, Mark Abraham <[email protected]> wrote: > On 21/11/2010 9:09 PM, pawan raghav wrote: >> >> Thank mark for comments, but I have check the structure after energy >> minimization through ramachandran plot and found 82% residues were lies in >> core region. After performed position restrained dynamics it reduced to 52% >> in core region also 1 bad contact was found. I have taken SPC water model >> then add 2 NA+ ions in the solvent, done energy minimization at emtol value >> of 2000 kJ/mol and steps for 250. Below is the pr.mdp file for position >> restraiuned dynamics, please let me know if any serious flaws. So help me by >> giving me the reference. >> >> title = Position restrained of Bcl-2. >> >> integrator = md >> >> define = -DPOSRES >> >> dt = 0.002 >> > > A smaller timestep during equilibration will better help the integration > cope with anything that is not very happy. > >> nsteps = 100000 >> >> nstcomm = 1 >> >> nstxout = 250 >> >> nstvout = 1000 >> >> nstfout = 0 >> >> nstlog = 10 >> >> nstenergy = 10 >> >> nstlist = 5 >> >> xtc_grps = protein sol >> >> energygrps = protein sol >> >> ns_type = grid >> >> rlist = 1.0 >> >> coulombtype = PME >> >> rcoulomb = 1.0 >> >> vdwtype = cut-off >> >> rvdw = 1.4 >> >> fourierspacing = 0.135 >> >> fourier_nx = 0 >> >> fourier_ny = 0 >> >> fourier_nz = 0 >> >> pme_order = 4 >> >> ewald_rtol = 1e-5 >> >> optimize_fft = yes >> >> Dispcorr = no >> >> Tcoupl = v-rescale >> >> tc-grps = protein sol NA+ >> > > Those groups are bad. See > http://www.gromacs.org/Documentation/Terminology/Thermostats > > Mark > >> tau_t = 0.1 0.1 0.1 >> >> ref_t = 300 300 300 >> >> Pcoupl = parrinello-rahman >> >> Pcoupltype = isotropic >> >> tau_p = 0.5 >> >> compressibility = 4.5e-5 >> >> ref_p = 1.0 >> >> gen_vel = yes >> >> gen_temp = 300.0 >> >> gen_seed = 173529 >> >> constraints = all-bonds >> >> >> >> -- >> Pawan > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
