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 >> 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
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