On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > On 4/27/12 12:09 PM, Steven Neumann wrote: > >> >> >> On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 4/27/12 11:34 AM, Steven Neumann wrote: >> >> >> >> On Fri, Apr 27, 2012 at 4:28 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> On 4/27/12 11:22 AM, Steven Neumann wrote: >> >> Dear Gmx Users, >> >> I am running 2 us simulation in implicit solvent model: >> >> define = -DPOSRES >> integrator = sd ; leap-frog integrator >> nsteps = 500000000 ; 0.004 * 500000000= 2 us >> dt = 0.004 ; 4 fs >> ; Output control >> nstxout = 0 >> nstxtcout = 50000 ; xtc compressed trajectory >> output >> every 2 ps >> nstenergy = 10000 ; save energies every 2 ps >> nstlog = 10000 ; update log file every 2 ps >> >> How come my trajectory (trr) is being created and takes 80 >> GB? >> >> >> The default for nstvout is 100, so you're likely getting very >> frequent >> output of velocities into the .trr file. >> >> -Justin >> >> Thank you >> This job crashed due to the quota exceeded. If change my mdp file >> (with >> additional nstvout=0) using tpbconv and run it from the >> checkpoint file it >> should work then with no trr file? >> >> >> If you need to change the .mdp file, you can't use tpbconv; use grompp >> to >> generate a new .tpr file and submit the new job. >> >> >> So if I will create new mdp file (with additional nstvout=0 to get rid of >> trr >> files) and use: >> >> mdrun -s new.tpr -cpi last.cpt >> >> Will I continue from the checkpoint? >> >> > That's the question I posed below... > > > I'm not sure if you can pick up using mdrun -cpi if the settings have >> changed, but you can try. >> >> >> Yes you can, from 4.0 you do not have to specify -append just -cpi file >> if the >> job crashed. >> >> > I am aware of checkpointing, but what I'm not sure of is if you change > output options (or others) mid-stream, if the checkpointing mechanism will > complain, particularly due to the changes in the .trr content. You'll have > to try and see. > > > -Justin > Indeed, it complains in terms of not present trr file (3 out of 4 files present) and he does not want to carry on. But when I change name of the output it starts from the checkpoint generating new files. Can I then somehow connect those two xtc trajectories using trjconv? Which tpr file I should use? Steven > > -- > ==============================**========== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > 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> >
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