[gmx-users] run g-msd using more than one core
Xiaobin Cao
xcao at lsu.edu
Wed Oct 22 21:56:57 CEST 2014
Dear GROMACS users,
I want to analyze the diffusion coefficient using g_msd. Can I run this command using more than one core, and how? I tried MPI version, but I can only use one core even I applied 16 cores on a supercomputer.
Thanks
_____________________________________________
Xiaobin Cao
Dept of Geology & Geophysics
E235, Howe-Russell Geosciences Complex,
Louisiana State University, Baton Rouge, LA 70803, U.S.A.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of gromacs.org_gmx-users-request at maillist.sys.kth.se <gromacs.org_gmx-users-request at maillist.sys.kth.se>
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Today's Topics:
1. Re: Fatal error:No molecules were defined in the system
(Nilesh Dhumal)
2. Re: Fatal error:No molecules were defined in the system
(Justin Lemkul)
3. Accelerated MD (Douglas Houston)
4. difference between Pulling and Acceleration? (Tom)
5. Calculating intermolecular water interactions (Jackson Chief Elk)
6. Re: Membrane simulations (lloyd riggs)
----------------------------------------------------------------------
Message: 1
Date: Mon, 20 Oct 2014 11:29:10 -0400
From: "Nilesh Dhumal" <ndhumal at andrew.cmu.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Fatal error:No molecules were defined in the
system
Message-ID:
<8529de0e7b39d0602ebbccda84ecbbf5.squirrel at webmail.andrew.cmu.edu>
Content-Type: text/plain;charset=iso-8859-1
I tried to send whole file.
File is big. Can I forward to your personal email directly?
Your mail to 'gromacs.org_gmx-users' with the subject
Re: [gmx-users] Fatal error:No molecules were defined in the
system
Is being held until the list moderator can review it for approval.
The reason it is being held:
Message body is too big: 58940 bytes with a limit of 50 KB
>
> On 10/20/14 11:19 AM, Nilesh Dhumal wrote:
>> Hello,
>>
>> For grompp
>>
>> grompp -f minim_hy.mdp -c cu.gro -p test.top -o 1.tpr
>>
>> I get the error" Fatal error:No molecules were defined in the system"
>>
>> Here I pasted initial part of test.top file.
>>
>>
>>
>>
>> ; Derived from parsing of runfiles/alat.top.orig
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 3 yes 0.5 0.5
>> ; comb-rule 3 is square-root sigma, the OPLSAA version
>>
>> [ atomtypes ]
>> ; full atom descriptions are available in ffoplsaa.atp
>> ; name bond_type mass charge ptype sigma epsilon
>> opls_991 Cu 29 63.54600 1.098 A 3.114e-01
>> 0.02092e+00
>> opls_993 OA 8 15.99940 -0.665 A 3.033e-01
>> 0.401664e+00
>> opls_994 OB 8 15.99940 -0.665 A 3.033e-01
>> 0.401664e+00
>> opls_995 CA 6 12.0110 0.778 A 3.473e-01
>> 0.39748e+00
>> opls_996 CB 6 12.0110 -0.092 A 3.473e-01
>> 0.39748e+00
>> opls_997 CC 6 12.0110 -0.014 A 3.473e-01
>> 0.39748e+00
>> opls_998 HM 1 1.0080 0.109 A 2.846e-01
>> 0.06276e+00
>>
>> [ moleculetype ]
>> ; Name nrexcl
>> BTC 3
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass
>> typeB
>> chargeB massB
>> 1 opls_993 1 BTC OA 1 -0.665 15.99940
>> 2 opls_995 1 BTC CA 2 0.778 12.01100
>> 3 opls_996 1 BTC CB 3 -0.092 12.01100
>> 4 opls_997 1 BTC CC 4 -0.014 12.01100
>> 5 opls_998 1 BTC HM 5 0.109 1.00800
>> 6 opls_997 1 BTC CC 6 -0.014 12.01100
>> 7 opls_998 1 BTC HM 7 0.109 1.00800
>> 8 opls_993 1 BTC OA 8 -0.665 15.99940
>> 9 opls_995 1 BTC CA 9 0.778 12.01100
>> 10 opls_996 1 BTC CB 10 -0.092 12.01100
>> 11 opls_997 1 BTC CC 11 -0.014 12.01100
>> 12 opls_998 1 BTC HM 12 0.109 1.00800
>> 13 opls_993 1 BTC OA 13 -0.665 15.99940
>> 14 opls_995 1 BTC CA 14 0.778 12.01100
>> 15 opls_996 1 BTC CB 15 -0.092 12.01100
>> 16 opls_994 1 BTC OB 16 -0.665 15.99940
>> 17 opls_994 1 BTC OB 17 -0.665 15.99940
>> 18 opls_994 1 BTC OB 18 -0.665 15.99940
>> 19 opls_993 1 BTC OA 19 -0.665 15.99940
>> 20 opls_995 1 BTC CA 20 0.778 12.01100
>>
>> Is there any error in .top file?
>>
>
> There is no way to tell unless you provide the full file. Either there is
> a
> syntax error somewhere that breaks the parsing, or your [molecules]
> section is
> empty.
>
> -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
>
> * Please search the archive at
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> posting!
>
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>
------------------------------
Message: 2
Date: Mon, 20 Oct 2014 11:31:05 -0400
From: Justin Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Fatal error:No molecules were defined in the
system
Message-ID: <54452AB9.5020004 at vt.edu>
Content-Type: text/plain; charset=windows-1252; format=flowed
On 10/20/14 11:29 AM, Nilesh Dhumal wrote:
> I tried to send whole file.
>
>
> File is big. Can I forward to your personal email directly?
>
No, the proper etiquette for sending files is to post them to a file-sharing
service and provide the link to the list.
-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
==================================================
------------------------------
Message: 3
Date: Mon, 20 Oct 2014 21:33:30 +0100
From: Douglas Houston <DouglasR.Houston at ed.ac.uk>
To: gmx-users at gromacs.org
Subject: [gmx-users] Accelerated MD
Message-ID: <20141020213330.74462skwlh1q5dic at www.staffmail.ed.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
format="flowed"
Hi all,
Can anyone recommend a book or (preferably) review article summarising
the various accelerated MD methods commonly used in protein/peptide
simulation these days? e.g. ABF, PLUMED, REMD, aMD etc. etc. I can
read about each individually but I could use a comprehensive but
concise comparison of their pros/cons and most popular applications.
cheers,
Doug
_____________________________________________________
Dr. Douglas R. Houston
Lecturer
Institute of Structural and Molecular Biology
Room 3.23, Michael Swann Building
King's Buildings
University of Edinburgh
Edinburgh, EH9 3JR, UK
Tel. 0131 650 7358
http://tinyurl.com/douglasrhouston
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
------------------------------
Message: 4
Date: Mon, 20 Oct 2014 18:47:47 -0500
From: Tom <dnaafm at gmail.com>
To: gmx-users <gmx-users at gromacs.org>
Subject: [gmx-users] difference between Pulling and Acceleration?
Message-ID:
<CAARYzz5MeZyVvPH8+R-XcbYs_oLrtv7nBYJyhKyNVv-0cpUqFw at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Dear Gromacs Developer,
In the version of 5.0 or later, Gromacs has the functionalities
of Non-equilibrium MD by assigning the group of acceleration.
I am confused what is the difference between this acceleration
and the previous functionality of Non-equilibrium Pulling.
Pulling is to pull the group center of mass.
Does NEMD/acceleration assign acceleration of each atoms (not
center of mass) inside the group, like some external field of gravity ?
Thanks a lot for the information!
Thomas
------------------------------
Message: 5
Date: Mon, 20 Oct 2014 18:57:20 -0600
From: Jackson Chief Elk <jchiefelk at gmail.com>
To: "gromacs.org_gmx-users at maillist.sys.kth.se"
<gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: [gmx-users] Calculating intermolecular water interactions
Message-ID: <F3317854-45EF-4D35-A2C7-877D378532A7 at gmail.com>
Content-Type: text/plain; charset=us-ascii
Hello,
I need to calculate the intermolecular interaction energy for water confined to a micro cavity I simulated in a biphasic water-bromobutane system. What I need to do is calculate the interaction energies ONLY for water that is within 0.4nm from the center-of-mass of the micro-cavity. Has anybody attempted to do this on their simulation data? I don't know where to start because g_energy does not give me what I need, and the documentation and examples of g_enemat are suboptimal.
Jackson
------------------------------
Message: 6
Date: Tue, 21 Oct 2014 05:40:21 +0200
From: "lloyd riggs" <lloyd.riggs at gmx.ch>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Membrane simulations
Message-ID:
<trinity-86812485-abcc-4631-86bc-18689d40d832-1413862821775 at 3capp-gmx-bs44>
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