> -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Nuno Azoia > Sent: Monday, July 08, 2013 11:21 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Stimulation stopped at 2ns > > 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. >
Did you already ran gmxdump on the tpr file you used? Then you will immediately see, how many steps are set in the tpr file. /Flo > > 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.or > g/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/S > upport/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 -- 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? 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