[gmx-users] The simulation of big protein in implicit solvent

[Yi Isaac Yang]

Thank you very much!

Now I know how to perform in serial mode. However, I still don't know how
to parallel perform the MD simulation. I have read the website you
recommended, but I still know how to change the domain decomposition
algorithm. I search the Internet, some people said add the flag -pd to
change to particle decomposition. However, in gromacs 5 the flag "-pd" have
been removed.

So do you know how to parallel perform the simulation in implicit solvent
using Gromacs 5?

Thank you and best regards,
Isaac


2016-09-01 15:30 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 9/1/16 9:28 AM, Yi Isaac Yang wrote:
>
>> Thank you very much! But I just perform the minimization in my own
>> computer:
>>
>> yangy at magadino:/mnt/storage2/yangy/l_repressor$ gmx mdrun -v -deffnm
>> lrepressor_min
>>
>>                    :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>>
>>                             GROMACS is written by:
>>      Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
>> Bjelkmar
>>  Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian
>> Fritsch
>>   Gerrit Groenhof   Christoph Junghans   Anca Hamuraru    Vincent
>> Hindriksen
>>  Dimitrios Karkoulis    Peter Kasson        Jiri Kraus      Carsten
>> Kutzner
>>     Per Larsson      Justin A. Lemkul   Magnus Lundborg   Pieter
>> Meulenhoff
>>    Erik Marklund      Teemu Murtola       Szilard Pall       Sander Pronk
>>    Roland Schulz     Alexey Shvetsov     Michael Shirts     Alfons Sijbers
>>    Peter Tieleman    Teemu Virolainen  Christian Wennberg    Maarten Wolf
>>                            and the project leaders:
>>         Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
>>
>> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>> Copyright (c) 2001-2015, The GROMACS development team at
>> Uppsala University, Stockholm University and
>> the Royal Institute of Technology, Sweden.
>> check out http://www.gromacs.org for more information.
>>
>> GROMACS is free software; you can redistribute it and/or modify it
>> under the terms of the GNU Lesser General Public License
>> as published by the Free Software Foundation; either version 2.1
>> of the License, or (at your option) any later version.
>>
>> GROMACS:      gmx mdrun, VERSION 5.1.2
>> Executable:   /home/yangy/opt/bin/gmx
>> Data prefix:  /home/yangy/opt
>> Command line:
>>   gmx mdrun -v -deffnm lrepressor_min
>>
>>
>> Running on 1 node with total 4 cores, 8 logical cores
>> Hardware detected:
>>   CPU info:
>>     Vendor: GenuineIntel
>>     Brand:  Intel(R) Xeon(R) CPU E3-1246 v3 @ 3.50GHz
>>     SIMD instructions most likely to fit this hardware: AVX2_256
>>     SIMD instructions selected at GROMACS compile time: AVX2_256
>>
>> Reading file lrepressor_min.tpr, VERSION 5.1.2 (single precision)
>>
>> -------------------------------------------------------
>> Program gmx mdrun, VERSION 5.1.2
>> Source code file:
>> /home/yangy/Downloads/gromacs-5.1.2-patched/src/gromacs/domd
>> ec/domdec.cpp,
>> line: 6542
>>
>> Fatal error:
>> Domain decomposition does not support simple neighbor searching, use grid
>> searching or run with one MPI rank
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>>
>> In fact, I'm not very familiar with gromacs, before that I always use
>> AMBER. So could you tell me how to perform mdrun with "one MPI rank"?
>> Although I directly run it in my own computer, it still show that "Running
>> on 1 node with total 4 cores, 8 logical cores". And what is "domain
>> decomposition"? Could I change it? Although I can perform the minimization
>> in serial mode,  I must using MPI to perform the MD simulation.
>>
>>
> Start here:
>
> http://www.gromacs.org/Documentation/Acceleration_and_parallelization
>
> The mdrun help description has all the rest of what you need to know (e.g.
> mdrun -ntmpi 1 in this case).
>
>
> -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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-- 
Yesterday Young
College of Chemistry and Molecular Engineering
Peking University