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

[Justin Lemkul]

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
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>   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:
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>
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2015, The GROMACS development team at
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> check out http://www.gromacs.org for more information.
>
> GROMACS is free software; you can redistribute it and/or modify it
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>
> 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/domdec/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

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