Please see the following pr.mdp and full.mdp pr.mdp
cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50000 ; total 100 ps. nstcomm = 1 nstxout = 500 nstvout = 1000 nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 500 500 ; Energy monitoring energygrps = Protein Non-protein ; Pressure coupling is not on Pcoupl = no tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 500 K. gen_vel = yes gen_temp = 500.0 gen_seed = 173529 full.mdp cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 50000000 ; total 100000 ps. nstcomm = 1 nstxout = 5000 nstvout = 40000 nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 ; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-protein tau_t = 0.1 0.1 ref_t = 500 500 ; Energy monitoring energygrps = Protein Non-protein ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is off at 500 K. gen_vel = no gen_temp = 500.0 gen_seed = 173529 Please tell me why protein shows unfolding in very first frame. msnayeem On 4/7/10, Mark Abraham <mark.abra...@anu.edu.au> wrote: > > On 7/04/2010 9:08 PM, shahid nayeem wrote: > >> Dear users >> Please let me know some basic question. I am sorry if I am asking a >> silly question. >> a) While simulating a protein thermal unfolding at high temperature say >> 500K should I run position restraint dynamics at 500k or at 298K. I am >> doing 100ps position restraint dynamics at 500k. Am I right in doing so. >> > > The usual purpose of position restrained MD is to allow the system to > achieve close to the ensemble desired for the start of the simulation > without perturbing the initial structure. > > b) While using Berendsen thermostat, how to select a value of tau_t and >> how does it affects simulation output. The same question for NoseHoover >> thermostat. >> > > Start by reading the GROMACS manual sections. > > c) After completing the 100ns simulation when I view the .xtc file in >> VMD I find that alpha helix of the protein is unfolded in very first >> frame collected at 10ps interval and reduced by trjconv at 50ps >> interval. Is it possible. If not then where I am wrong. >> I did Steepest descent minimization, then 100ps position restraint >> Dynamics at 500K and then 100ns full dynamics at 500k. >> > > 10ps would be very fast for a lengthy helix to unfold, however you've > deliberately taken your force field out of the zone where it was > parameterized, so we can't really infer anything about its behaviour. You > could also have a broken model physics in your .mdp file, but we can't know > about that. > > The real lesson here is not to do a lengthy simulation without looking at > the early and ongoing results. > > 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/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/mailing_lists/users.php >
-- 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/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/mailing_lists/users.php
