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

Justin Lemkul jalemkul at vt.edu
Thu Sep 1 15:31:06 CEST 2016

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 (-:
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> Bjelkmar
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>  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
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> 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:


The mdrun help description has all the rest of what you need to know (e.g. mdrun 
-ntmpi 1 in this case).



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


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