[gmx-users] The simulation of big protein in implicit solvent
Yi Isaac Yang
yesterday.young at gmail.com
Thu Sep 1 16:46:58 CEST 2016
Alright ....
But I don't think It is not the fault of GB model. If you want to perform a
simulation in vacuum it will also case this problem.
Thanks a lot!
2016-09-01 16:37 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>>>>
>>>> ==================================================
>>>> --
>>>> Gromacs Users mailing list
>>>>
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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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> Gromacs Users mailing list
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--
Yesterday Young
College of Chemistry and Molecular Engineering
Peking University
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