that means generating a trajectory file for every 10 steps rite then i may need more disk space
On Tue, Apr 20, 2010 at 11:41 PM, XAvier Periole <x.peri...@rug.nl> wrote: > > On Apr 20, 2010, at 7:39 PM, Bharath.K. Chakravarthi wrote: > > no i did not used -v flag at that command may be thats the mistake > thank u Justin > > On Tue, Apr 20, 2010 at 10:54 PM, Justin A. Lemkul <jalem...@vt.edu>wrote: > >> >> >> Bharath.K wrote: >> >>> I'm using gromacs-3.3.3 and here is the parameter >>> >>> .. >>> .. >>> nstxout = 500 >>> nstvout = 1000 >>> nstfout = 0 >>> nstlist = 100 >>> >> This might not be the best choice! it is generally kept under 10! It > depends on your > system/force field though.... > > nstlog = 100 >>> nstenergy = 10 >>> nstxtcout = 500 >>> .. >>> .. >>> >>> for writing trajectories in .mdp file and what is check point file and >>> -cpi file.cpt ... >>> i did not get u.... :( >>> >>> >> This is why stating your Gromacs version at the outset is useful. >> Checkpointing was introduced in Gromacs 4.0, so you won't be able to use >> it. >> >> You also have not answered my first question. What is your mdrun command >> line? Did you use the -v flag? If not, you will not get any information >> about completion time. There is nothing that the .mdp options or tpbconv >> will do for you as far as completion time is concerned. >> >> -Justin >> >> >> On Tue, 20 Apr 2010 22:20:35 +0530, XAvier Periole <x.peri...@rug.nl> >>> wrote: >>> >>> >>>> >>>>> >tpbconv -s md.tpr -f md_traj.chk.trr -o md_01.tpr -until 1000 >>>>> this shows last step before crashing and starts from there until 1000 >>>>> >>>>> >>>> then >>>>> >>>>> >mdrun -s md_01.tpr -o md_traj_01.trr -c minim_water.gro -g md.log - >>>>> e minim_ener_01.edr >>>>> >>>>> >>>> Nothing seem particularly wrong! May be you write your trajectory file >>>> too often! Did the original the indicated the same amount of data to be >>>> written? >>>> >>>> which version of gmx you are using? actually using the check point >>>> file is relatively easy (-cpi fie.cpt to add to mdrun) and does all >>>> the work for you! >>>> >>>>> >>>>> >>>> >>>> >>>>> On Tue, Apr 20, 2010 at 7:50 PM, XAvier Periole <x.peri...@rug.nl> >>>>> wrote: >>>>> >>>>> On Apr 20, 2010, at 9:14 AM, Bharath.K wrote: >>>>> >>>>> Hello all.... >>>>> i got a system crash at some steps.. >>>>> after creating the new .trr file using command tpbconv >>>>> trr file with tpbconv? you mean tpr? >>>>> and running MDS >>>>> what is MDS? >>>>> >>>>> by mdrun command the approximate finishing time is not showing..... >>>>> and also a warning is showing as >>>>> >>>>> WARNING: this run may generate approximately 4583292 Mb of data.... >>>>> That is a bit enormous >>>>> >>>>> >>>>> is there any changes that i should do while giving the command and >>>>> can i continue with this warning..... >>>>> Which exact command did you use? >>>>> >>>>> >>>>> >>>>> -- >>>>> Bharath.K >>>>> Ph-9535629260 >>>>> -- >>>>> 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/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use thewww >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> -- >>>>> 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/search before >>>>> posting! >>>>> Please don't post (un)subscribe requests to the list. Use thewww >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>>>> >>>>> >>>>> >>>>> -- >>>>> Bharath.K.Chakravarthi >>>>> Ph:9535629260 >>>>> -- >>>>> 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/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/mailing_lists/users.php >>>>> >>>> >>>> >>> >>> >> -- >> ======================================== >> >> 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/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/mailing_lists/users.php >> > > > > -- > Bharath.K.Chakravarthi > Ph:9535629260 > -- > 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/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/mailing_lists/users.php > > > > -- > 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/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/mailing_lists/users.php > -- Bharath.K.Chakravarthi Ph:9535629260
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