[gmx-users] membed in mdrun VERSION 5.0.4

[Nash, Anthony]

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-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
>>>>
>>>> ==================================================
>>>> --
>>>> 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-request at 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-request at 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-request at 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-request at gromacs.org.