[gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

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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