Hi, You're right that mdrun -membed is only implemented for one rank - there's a fatal error message that you doubtless have already seen.
On Sat, Jan 9, 2016 at 5:32 PM Nash, Anthony <a.n...@ucl.ac.uk> wrote: > 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. > Yeah, there's a message printed to stderr that this is deliberate, because restart is not supported either. 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. > It doesn't matter which molecules from a set of identical ones are removed, so long as the atom ordering of the resulting system is the same. Mark > 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? 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