Sorry for the typo. grompp -f md.mdp -c npt.gro -p complex.top -t npt.cpt -o md.tpr
This is fine, right? Thanks very much Justin for confirming the mdp file opions.. On Fri, Apr 18, 2014 at 2:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > 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. > -- Ankita Naithani -- 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.