Hi, Just to add to my earlier message, I went through all release notes after 5.0.4, and besides a change in membed documentation, I can’t see a reference to a parallelized version of mdrun -membed.
Thanks Anthony On 08/01/2016 23:36, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@ucl.ac.uk> wrote: >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? 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