On 4/18/14, 8:55 AM, Ankita Naithani wrote:
Thank you Justin for your reply. Yes indeed this is a production run. So would the following mdp file be okay now? title = production MD ; Run parameters integrator = md ; leap-frog algorithm nsteps = 50000000 ; 0.002 * 50000000 = 100000 ps or 100 ns dt = 0.002 ; 2 fs ; Output control nstxout = 0 ; save coordinates every 2 ps nstvout = 0 ; save velocities every 2 ps nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps nstenergy = 1000 ; save energies every 5 ps nstlog = 1000 ; update log file every 5 ps ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constraine d lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 25 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) rlistlong = 1.0 ; long-range neighborlist cutoff (in nm) cutoff-scheme = Verlet ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostat ics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT nstcomm = 10 ; remove com every 10 steps ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 318 318 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = Parrinello-Rahman ; pressure coupling is on for NP T pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; Velocity generation is off gen_temp = 318 ; reference temperature, for protein in K grompp -f md.mdp -c npt.gro -p complex.top -o md.tpr? Could you please advice?
The grompp command is incorrect. As I said before, if you want to preserve the work of the previous equilibration, you need to pass the .cpt file from the previous step with grompp -t.
Otherwise, provided the cutoffs are correct for your chosen force field, the .mdp file looks reasonable.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
