My apologies that this hasn’t made it into one large message. I would like to add two further points. It appears as though mdrun (serial) does not output a .cpt file when -membed is specified. I just ran out of clock time, and the check point file is just not there.
Also, in response to your earlier comment about using gmx convert-tpr, -membed appears to remove some lipids and solvent molecules but it won’t tell you which ones until you have the final .gro file. Therefore, I don’t believe I can make a .ndx to use with gmx-convert-tpr. Thanks Anthony On 09/01/2016 09:28, "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: >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? 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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