-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello,
I haven't read the mails before, but as long as you are not in equilibrium I do not think that PR coupling is the best way to go. Furthermore PR is very sensitive to constraints and the time step, so perhaps 2fs is too large. Try to perform a simulations with the Berendsen thermostat to reach equilibrium and from there on turn on the PR coupling. Perhaps it is also a good idea to combine Parrinello-Rahman with the Nose-Hoover coupling scheme for the temperature as they are very similar. /Flo On 11/21/2010 11:09 AM, 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 > > 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+ > > 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 > - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzpDx4ACgkQLpNNBb9GiPm4pwCgnELG6jRU8HNptP9v7NzC++Uy 6SMAnRodoGiNjdvcnM4NQdyLmwt17w4y =VgDX -----END PGP SIGNATURE----- -- 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