[gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

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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