I think it might be more illustrative to understand why you think two different systems will necessarily run at the same speed. How large is the protein/water system? If it is a billion atoms and you expect it to run as fast as a system containing only several thousand (running on the same number of processors), then you would almost certainly be mistaken.
Also, note that in our temperature coupling section, you should not couple solvent and ions separately. See here: http://wiki.gromacs.org/index.php/Thermostats -Justin Quoting sudheer <[EMAIL PROTECTED]>: > > Thanks for response Mr.Alan Dodd > 1) 1st run is simularion of position restrain of protein in water (25000 > steps) - system running very very slow means for completion 10 steps it is > taking more than 5 minutes or more > 2) 2nd simulation is production step of popc in water (125000 steps ) - this > is going normally means for completion 10 steps it is taking 3seconds or less > than that. > i will send you the both input files of pr.mdp and md.mdp files > > pr.mdp file ( This is already sent) > title = Yo > cpp = /usr/bin/cpp > define = -DPOSRES > constraints = all-bonds > integrator = md > dt = 0.002 > nsteps = 25000 > nstcomm = 1 > nstxout = 50 > nstvout = 1000 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > pbc = xyz > ; Berendsen temperature coupling is on in two groups > ; Pressure coupling is on > Tcoupl = berendsen > tc-grps = Protein SOL Na+ > tau_t = 0.1 0.1 0.1 > ref_t = 300 300 300 > Pcoupl = parrinello-rahman > pcoupltype = isotropic > ref_p = 1 > tau_p = 0.5 > compressibility = 4.5e-5 > ; Energy monitoring > energygrps = Protein SOL Na+ > ; Generate velocites is on at 300 K. > gen_vel = yes > gen_temp = 300.0 > gen_seed = 173529 > > > md.mdp file > cpp = /lib/cpp > constraints = all-bonds > integrator = md > dt = 0.002 ; ps ! > nsteps = 125000 ; total 250 ps. > nstcomm = 1 > nstxout = 50 > nstvout = 10 > nstfout = 0 > nstlog = 10 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.0 > rcoulomb = 1.0 > rvdw = 1.0 > pbc = xyz > ; Berendsen temperature coupling is on in two groups > Tcoupl = berendsen > tc-grps = POPC SOL > tau_t = 0.1 0.1 > ref_t = 300 300 > ; Energy monitoring > energygrps = POPC SOL > ; 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 300 K. > gen_vel = no > gen_temp = 300.0 > gen_seed = 173529 > > > > pls anyone help me > thanks in advance....... ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php