[gmx-users] The simulation of big protein in implicit solvent
Justin Lemkul
jalemkul at vt.edu
Thu Sep 1 16:37:35 CEST 2016
On 9/1/16 10:35 AM, Yi Isaac Yang wrote:
> Thank you very much!
>
> But when I using this command:
>
> gmx mdrun -ntomp 4 -ntmpi 1 -deffnm lrepressor_bal
>
> It shows:
> Fatal error:
> 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
>
Hence you see our reason for removing GB in the future. It's incompatible with
too many features. Looks like you're stuck running in serial. That's probably
inefficient for most purposes.
-Justin
>
> 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,
>> 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
>>
>
>
>
--
==================================================
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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