Thanks Justin very much for your help. (Extremely silly and unthoughtful of me to forget this)
Kind regards, Ankita On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/4/13 7:37 AM, Ankita Naithani wrote: > >> I do have the .mdp file. Main thing I was concerned about were details >> like >> number of water molecules added and number of counter ions added. Does >> gmxdump output that information? >> >> > Yes, buried in a long list of other things. Trivial details like that are > simply read from the last few lines of the .top though, so there's no need > to invoke any other accessory programs. > > -Justin > > > >> >> >> On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 11/4/13 7:14 AM, Ankita Naithani wrote: >>> >>> Hi Justin, >>>> >>>> Thank you for your reply. I did give the .tpr file but the job >>>> terminated >>>> after few frames only. Also, if that is not helpful, do you have any >>>> >>>> >>> There are no frames in a .tpr file. I suspect you're simply issuing the >>> command incorrectly, but since you haven't shown us what you're doing, >>> there's little else to suggest. >>> >>> >>> suggestions to recover the essential information which you would >>> include >>> >>>> as >>>> part of methods? >>>> >>>> >>>> The .mdp file has all the instructions for the simulation. If you >>> don't >>> have that around for whatever reason (very bad to get rid of such >>> files!), >>> all of the same information is recorded in the beginning of the .log file >>> or can be written out by gmxdump. In the latter case, make sure to >>> redirect the output to a file rather than just have thousands of lines of >>> text blur by in the terminal. >>> >>> >>> -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 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> >>> ================================================== >>> -- >>> 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 >>> >>> >> >> >> > -- > ================================================== > > 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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > ================================================== > -- > 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 > -- Ankita Naithani -- 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
