[gmx-users] mdrun -membed Sorry, parallel g_membed is not yet fully functional.

[Justin Lemkul]

On 7/22/16 10:54 AM, -Mario wrote:
> I confirm that it worked smoothly by adding this command.
> I think I guessed the role of the command -nt 1, correct me if I'm
> mistaken: running on single thread avoids parallelization thus it gives no
> error.
>

Correct.

> Now another great problem is that in the original study a .gro file is
> supposed to be produced, but I can only see .edr and .log.
> Don't know if I'm getting it wrong or something.
>

It's running a pseudo-simulation to embed the protein.  You'll eventually get a 
coordinate file, but depending on how large the system is, it will probably take 
a while since you can't run in parallel.

-Justin

> Thanks deeply for your  help.
>
> -Mario
>
>
> 2016-07-21 23:29 GMT+02:00 -Mario <marios9.mf at gmail.com>:
>
>> I'm trying to insert a protein in membrane using the g_membed method, even
>> though this command is now integrated in MDRUN as far I understand.
>> Everything's ready, but when I run the mdrun with command:
>>
>>   gmx mdrun -deffnm input -membed embed.dat
>>
>> this error message occurs:
>>    Program gmx mdrun, VERSION 5.1.2
>>    Source code file: /home/mario/Scaricati/gromacs-
>>  5.1.2/src/programs/mdrun/membed.c, line: 1079
>>
>>    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
>>
>> Could please someone help?
>> Thanks in advance
>>
>> --
>> *Mario Falsaperna*
>>
>
>
>

-- 
==================================================

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

==================================================