Hi Priya, Does it help if you set
tcoupl = v-rescale Please read the manual, follow a tutorial properly, and think about what you're doing and what you get out. Cheers, Tsjerk On Jan 7, 2012 8:54 AM, "priya thiyagarajan" <priya.thiyagaraja...@gmail.com> wrote: hello sir, i followed lysozyme tutorial to do dynamics for my protein.. but at the end of NVT equilibration, my temperature is at 243K.. but i set 300K to my mdp file .. mine is not getting equilibrium condition.. this is my nvt.mdp file title =GROMOS43a1 lipopeptide NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 100000 ; 2 * 100000 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = No ; modified Berendsen thermostat tc-grps = DRG SOL ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed may i know what is the reason.. initially i did nvt for 100ps but i didnt get equil temperature. then i increased my time to 200ps.. still i am not getting.. help me with your answer.. Thanking you, -- 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
-- 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
