Thanks a lot for the quick reply...................probably I have overlooked this point earlier ..........now I'm getting it properly........
On Thu, Aug 16, 2012 at 10:33 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/16/12 12:57 PM, tarak karmakar wrote: >> >> Dear All, >> >> In my simulation I want the temperature of the system to be reached at >> 300 K only after 3 ps. But after 3ps I see temperature became 402 K. >> So am I doing any mistake in the '.mdp' file given below? >> > > You have a few. > > 1. You should not run MD with flexible water. > 2. Finite cutoffs lead to rounding errors and accumulation of heat. This is > most likely the source of your problem. I seem to recall Mark (or maybe > someone else) already told you about this point. > > -Justin > > >> define = -DFLEXIBLE >> constraints = h-bonds >> integrator = sd >> dt = 0.001 ; 1fs >> nsteps = 3000 ; 3ps >> nstcomm = 1 >> nstxout = 1000 ; frequency to write coordinates >> to output trajectory >> nstvout = 0 ; frequency to write velocities >> to output trajectory; the last velocities are always written >> nstfout = 0 ; frequency to write forces to >> output trajectory >> nstlog = 10 ; frequency to write energies to >> log file >> nstenergy = 100 ; frequency to write energies to edr file >> nstcalcenergy = 100 >> vdwtype = cut-off >> coulombtype = cut-off >> pbc = no >> table-extension = 20.0 >> nstlist = 100 >> ns_type = grid >> rlist = 1.0 >> >> rcoulomb = 1.2 >> rvdw = 1.2 >> >> comm-mode = angular >> comm-grps = system >> optimize_fft = yes >> >> ;heating >> annealing = single >> annealing_npoints = 2 >> annealing_time = 0 3 >> annealing_temp = 0 300 >> >> ld_seed = 8072012 >> >> ;temperature coupling is on >> Tcoupl = berendsen >> tau_t = 0.01 >> tc_grps = system >> ref_t = 0 >> >> ;Pressure coupling is off >> Pcoupl = no >> >> ; Generate velocites is on >> gen_vel = yes >> gen_temp = 0 >> gen_seed = 8042012 >> >> >> >> Thanks, >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 -- Tarak Karmakar Molecular Simulation Lab. Chemistry and Physics of Materials Unit Jawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O. Bangalore - 560 064 Karnataka, INDIA Ph. (lab) : +91-80-22082809 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
