On Mon, Apr 30, 2012 at 9:39 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 30/04/2012 6:34 PM, Steven Neumann wrote: > > > > 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. > > > Yes, that will be the effect of the (default) mdrun -append yes in 4.5 > > > Can I then somehow connect those two xtc trajectories using trjconv? > > > Yes, or better trjcat. Be sure to read and understand their -h output > first. > > > Which tpr file I should use? > > > You don't even need a .tpr file to concatenate trajectory files. > > Mark > > Thank you Mark! Steven > > 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 >> >> ======================================== >> -- >> 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? Read http://www.gromacs.org/Support/Mailing_Lists >
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