Below is my .mdp file. The timestep dt shows as 0.001 ps title = protein cpp = /lib/cpp ; RUN CONTROL integrator = md nsteps = 3000000 dt = 0.001 ; NEIGHBOR SEARCHING nstlist = 10 ns_type = grid pbc = xyz rlist = 0.9 ; OUTPUT CONTROL nstxout = 500 nstvout = 500 nstxtcout = 0 nstlog = 10 constraints = all-bonds nstenergy = 100 ; OPTION FOR ELECTROSTATIC AND VDW coulombtype = PME rcoulomb_switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field epsilon_r = 1 ; Method for doing Van der Waals vdw-type = Cut-off ; cut-off lengths rvdw_switch = 0 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = No ; Extension of the potential lookup tables beyond the cut-off table-extension = 2.5 ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.28 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps = SOL Protein Na tau_t = 0.1 0.1 0.1 ref_t = 300 300 300 Pcoupl = Berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300
-- Chandan kumar Choudhury NCL, Pune INDIA On Tue, Feb 16, 2010 at 11:27 PM, Mark Abraham <[email protected]>wrote: > On 17/02/10 04:43, Chandan Choudhury wrote: > >> Thanks Justin !! >> But my state_prev.cpt file shows >> $gmxcheck -f state_prev.cpt >> >> Checking file state_prev.cpt >> >> # Atoms 186864 >> Last frame -1 time 9346.700 >> >> >> Item #frames Timestep (ps) >> Step 1 >> Time 1 >> Lambda 1 >> Coords 1 >> Velocities 1 >> Forces 0 >> Box 1 >> >> Here also the time is greater than the .trr file. >> >> Cant understand how to overcome it. >> > > Your checkpoint interval need not match your .trr-writing interval - see > your .mdp file. > > > Mark > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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