On 8 July 2013 22:12, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/8/13 5:08 PM, Rama Krishna Koppisetti wrote: > >> Thanks Justin for your reply, >> >> I found something like this, in .log file,nsteps=1000000 but in .mdp file >> > > Then you're not using the .mdp file you think you are and the run is only > scheduled for 2 ns.
After changing the .mdp file, did you run grompp again? And did you get a new .tpr file? I already had a similar problem. Sometimes; and I not sure about the gromacs version on that time, I just run grompp with new parameters in the .mdp file but grompp did not change the .tpr file, if already present. Cheers Nuno Azoia > > > it is nsteps=5000000. I don't see any stdout and stderr files. >> >> > These are standard streams, not files. Some queuing systems and other > software save their output, others don't. > > -Justin > > > ______________________________**_________________________ >> 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<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 <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> >>> <htt**p://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<h**ttp://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> >>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>> > >>> >>> > -- > ==============================**==================== > > > 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> > -- Nuno Gonçalo Azoia Lopes Rua Nascente, nº 25 4705-473 Escudeiros Tel: 253 683 198 Móvel: 965 382 487 -- 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
