Thanks Justin for your reply, I found something like this, in .log file,nsteps=1000000 but in .mdp file it is nsteps=5000000. I don't see any stdout and stderr files.
_______________________________________________________ On Mon, Jul 8, 2013 at 3:50 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/8/13 4:33 PM, Rama wrote: > >> Dear All, >> >> I'm trying to do long stimulation run but every time it stops at 2ns, >> below >> pasted .mdp file parameters. How to run 10ns or more ns stimulation run? >> Do >> I need to change any parameters in .mdp file or else where. >> >> > There is nothing in the .mdp file that would cause the run to stop. > Either the simulation is crashing or you have some queuing system that is > terminating the job. Check stdout, stderr, and .log file(s) for > information. > > -Justin > > > Thanks in Advance. >> ------------- >> >> title = Protein-DMPC bilayer Production MD >> ; Run parameters >> integrator = md ; leap-frog integrator >> nsteps = 5000000 ; 2 * 5000000 = 10000 ps (10 ns) >> dt = 0.002 ; 2 fs >> ; Output control >> nstxout = 100000 ; save coordinates every 200 ps >> nstvout = 100000 ; save velocities every 200 ps >> nstxtcout = 50000 ; xtc compressed trajectory output every >> 100 ps >> nstenergy = 50000 ; save energies every 100 ps >> nstlog = 100000 ; update log file every 200 ps >> ; Bond parameters >> continuation = yes ; Restarting after NPT >> 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 cels >> nstlist = 5 ; 10 fs >> rlist = 1.2 ; short-range neighborlist cutoff (in nm) >> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.2 ; 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 = Nose-Hoover ; More accurate thermostat >> tc-grps = CA_ZN_DMPC_Protein SOL_CL ; three coupling groups - >> more accurate >> tau_t = 0.5 0.5 >> ; time >> constant, in ps >> ref_t = 310 310 >> ; reference >> temperature, one for each group, in K >> ; Pressure coupling is on >> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT >> pcoupltype = semiisotropic ; uniform scaling of x-y box >> vectors, >> independent z >> tau_p = 2.0 ; time constant, in ps >> ref_p = 1.0 1.0 ; reference pressure, >> x-y, z (in bar) >> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, >> 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 >> ; COM motion removal >> ; These options remove motion of the protein/bilayer relative to the >> solvent/ions >> nstcomm = 1 >> comm-mode = Linear >> comm-grps = Protein_DMPC SOL_CL >> >> >> >> >> -- >> View this message in context: http://gromacs.5086.x6.nabble.** >> com/Stimulation-stopped-at-**2ns-tp5009669.html<http://gromacs.5086.x6.nabble.com/Stimulation-stopped-at-2ns-tp5009669.html> >> Sent from the GROMACS Users Forum mailing list archive at Nabble.com. >> >> > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Associate > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
