[gmx-users] membed in mdrun VERSION 5.0.4

Wed Jan 13 22:56:45 CET 2016

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.nash at 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-bounces at maillist.sys.kth.se on
> behalf of Nash, Anthony"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> a.nash at 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-bounces at maillist.sys.kth.se
> on
> >behalf of Nash, Anthony"
> ><gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> >a.nash at 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-bounces at maillist.sys.kth.se
> >>on
> >>behalf of Mark Abraham"
> >><gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> >>on behalf of mark.j.abraham at 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 <jalemkul at 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
> >>>>
> >>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>>> http://mackerell.umaryland.edu/~jalemkul
> >>>>
> >>>> ==================================================
> >>>> --
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