You're welcome On 28 Oct 2013, at 20:03, Pavan Ghatty <pavan.grom...@gmail.com> wrote:
> Aah yes of course. Thanks James. > > > > On Mon, Oct 28, 2013 at 3:16 PM, <jkrie...@mrc-lmb.cam.ac.uk> wrote: > >> No this isn't a problem. You can use job names under the -hold_jid flag. >> As long as you change the job name in the submit script between >> submissions this isn't a problem. You could have a submit script for job 4 >> with -N md_job4 and -hold_jid md_job3 then change these to -N md_job5 and >> -hold_jid md_job4 for the next job. Then you can submit job 5 as soon as >> you have made this change which will be within seconds of submitting job >> 4. >> >>> Mark, >>> >>> The problem with one .tpr file set for 100ns is that when job number >> (say) >>> 4 hits the wall limit, it crashes and never gets a chance to submit the >>> next job. So it's not really automated. >>> >>> Now I could initiate job 5 before /mdrun/ in job 4's script and hold job >> 5 >>> till job 4 ends. But the PBS queuing system is sometime weird and takes a >>> bit of time to recognize a job and give back its jobID. So I could submit >>> job 5 but be unable to change its status to /hold/ because PBS does not >>> return its ID. Another problem is that if resources are available, job 5 >>> could start before I ever get a chance to /hold/ it. >>> >>> >>> >>> >>> On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham >>> <mark.j.abra...@gmail.com>wrote: >>> >>>> On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty <pavan.grom...@gmail.com >>>>> wrote: >>>> >>>>> I have need to collect 100ns but I can collect only ~1ns (1000steps) >>>> per >>>>> run. Since I dont have .trr files, I rely on .cpt files for restarts. >>>> For >>>>> example, >>>>> >>>>> grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 >>>>> >>>>> This runs into a problem when the run gets killed due to walltime >>>> limits. I >>>>> now have a .xtc file which has run (say) 700 steps and a .cpt file >>>> which >>>>> was last written at 600th step. >>>> >>>> You seem to have no need to use grompp, because you don't need to use a >>>> workflow that generates multiple .tpr files. Do the equivalent of what >>>> the >>>> restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a >>>> .tpr >>>> for the whole 100ns run, and then keep doing >>>> >>>> mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime >>>> >>>> with or without -append, perhaps with -maxh, keeping whatever manual >>>> backups you feel necessary. Then perhaps concatenate your final >>>> trajectory >>>> files, according to your earlier choices. >>>> >>>> - To set up the next run I use the .cpt file from 600th step. >>>>> - Now during analysis if I want to center the protein and such, >>>> /trjconv/ >>>>> needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ >>>> know >>>>> to stop at 600th step? >>>> >>>> >>>> trjconv just operates on the contents of the trajectory file, as >>>> modified >>>> by things like -b -e and -dt. The .tpr just gives it context, such as >>>> atom >>>> names. You could give it a .tpr from any point during the run. >>>> >>>> Mark >>>> >>>> If this has to be put in manually, it becomes >>>>> cumbersome. >>>>> >>>>> Thoughts? >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul <jalem...@vt.edu> >>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> On 10/27/13 9:37 AM, Pavan Ghatty wrote: >>>>>> >>>>>>> Hello All, >>>>>>> >>>>>>> Is there a way to make mdrun put out .cpt file with the same >>>> frequency >>>>> as >>>>>>> a >>>>>>> .xtc or .trr file. From here >>>>>>> http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts< >>>>> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts>I see >> that >>>> we >>>>>>> can choose how often (time in mins) the .cpt file is written. But >>>>> clearly >>>>>>> if the frequency of output of .cpt (frequency in mins) and .xtc >>>>> (frequency >>>>>>> in simulation steps) do not match, it can create problems during >>>>> analysis; >>>>>>> especially in the event of frequent crashes. Also, I am not storing >>>> .trr >>>>>>> file since I dont need that precision. >>>>>>> I am using Gromacs 4.6.1. >>>>>> What problems are you experiencing? There is no need for .cpt >>>> frequency >>>>>> to be the same as .xtc frequency, because any duplicate frames >>>> should >>>> be >>>>>> handled elegantly when appending. >>>>>> >>>>>> -Justin >>>>>> >>>>>> -- >>>>>> ==============================**==================== >>>>>> >>>>>> Justin A. Lemkul, Ph.D. >>>>>> Postdoctoral Fellow >>>>>> >>>>>> 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/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 >>>> -- >>>> 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 >> >> >> -- >> 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 -- 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
