[gmx-users] The simulation of big protein in implicit solvent
Yi Isaac Yang
yesterday.young at gmail.com
Thu Sep 1 16:35:32 CEST 2016
Thank you very much!
But when I using this command:
gmx mdrun -ntomp 4 -ntmpi 1 -deffnm lrepressor_bal
OpenMP threads have been requested with cut-off scheme Group, but these are
only supported with cut-off scheme Verlet
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
However, pbc=no have not be supportted by cut-off scheme=verlet
2016-09-01 16:20 GMT+02:00 Yi Isaac Yang <yesterday.young at gmail.com>:
> 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,
> 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
>>> yangy at magadino:/mnt/storage2/yangy/l_repressor$ gmx mdrun -v -deffnm
>>> :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>>> GROMACS is written by:
>>> Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
>>> Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian
>>> Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent
>>> Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten
>>> Per Larsson Justin A. Lemkul Magnus Lundborg Pieter
>>> Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
>>> Roland Schulz Alexey Shvetsov Michael Shirts Alfons
>>> 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:
>>> 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
>>> 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
>>> on 1 node with total 4 cores, 8 logical cores". And what is "domain
>>> decomposition"? Could I change it? Although I can perform the
>>> 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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> Yesterday Young
> College of Chemistry and Molecular Engineering
> Peking University
College of Chemistry and Molecular Engineering
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