Justin and Mark, many thanks for your help. With regards to the parallelization, when did parallel membed become supported? I¹ve just tried on 5.0.4 and I¹m getting the response:
Reading file membed_NPT_B.tpr, VERSION 5.0.4 (double precision) ------------------------------------------------------- Program mdrun_mpi_d, VERSION 5.0.4 Source code file: /dev/shm/tmp.3LEFQsSzrx/gromacs-5.0.4/src/programs/mdrun/membed.c, line: 1056 Input error or input inconsistency: Sorry, parallel g_membed is not yet fully functional. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Error on rank 0, will try to stop all ranks Halting parallel program mdrun_mpi_d on CPU 0 out of 2 Oh course, I understand this could be answered by installing the latest version, but I¹m ruling out anything I¹ve done wrong before asking central IT to put up a test module. Thanks for the help Anthony On 08/01/2016 13:24, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Mark Abraham" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of mark.j.abra...@gmail.com> wrote: >Hi, > >The current implementation of membed is quite sane and should support all >kinds of parallelization. (It is difficult to say much that is nice about >the first implementation, though!) > >gmx trjconv and convert-tpr are good for making subsets from well chosen >index groups. > >Mark > >On Fri, 8 Jan 2016 13:35 Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 1/8/16 3:38 AM, Nash, Anthony wrote: >> > Many thanks Justin, that¹s solved it. >> > >> > The simulation is now running, reporting that 8 POPC molecules and 12 >>SOL >> > molecules have been removed. However, I have a bit of a problem. I >>don¹t >> > seem to be able to get the -membed option working on a parallel >> > installation of gromacs, only serial. I assume parallel isn¹t >>supported? >> > >> >> No idea, but the -membed incorporation into mdrun is currently a very >>big >> hack >> to make it work, so you should expect limited support for features. >> >> > Secondly, with my .tpr file very different from my running .trr (due >>to >> > removed molecules), I don¹t know of a way of pulling out a single >>frame >> > from the trajectory to see how the simulation is progressing. (I would >> > have just taken the first frame as a .gro, downloaded the latest .trr, >> and >> > thrown them both into VMD). Any thoughts? >> > >> >> Does the program report which residues were removed? If so, you can >>just >> remove >> those from the coordinate file you had before. Otherwise, no, probably >> not. >> Like I said, big hack to get it working in the present version. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.