[gmx-users] Re: gmx-users Digest, Vol 58, Issue 125

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 24 03:00:37 CET 2009



akalabya bissoyi wrote:
> hello everybody
> thank you for u suggestion,  as i am new to Linux. so i am facing 
> problem in find out my working directory.

"Working directory" refers to whatever directory you are in.

> what is the universal path location of gromac in ubantu 8.10  where i 
> can type my command for execute the programme.

If you installed via Synaptic, then things will be all over the place - 
executables probably in /usr/bin, libraries in /usr/lib, topologies in 
/usr/share/gromacs/top, etc.

There is no single command to execute Gromacs, it is a software package.  As I 
advised before, read the manual and search for tutorials (there are some linked 
on wiki.gromacs.org - start there!).

Get some reference materials on learning Linux before trying to learn both Linux 
and Gromacs at the same time.  For a new user to both, it can be frustrating and 
unproductive.

-Justin

> plz help me regarding finding working directory.
> 
> On Tue, Feb 24, 2009 at 2:41 AM, <gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>> wrote:
> 
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>     Today's Topics:
> 
>       1. gromac running in ubantu 8.10 (akalabya bissoyi)
>       2. Re: gromac running in ubantu 8.10 (Justin A. Lemkul)
>       3. Turning off electrostatic or Van der Waals interactions (Lee Soin)
>       4. Re: Turning off electrostatic or Van der Waals    interactions
>          (Justin A. Lemkul)
>       5. Re: Turning off electrostatic or Van der Waals    interactions
>          (Lee Soin)
>       6. Re: Turning off electrostatic or Van der  Waals   interactions
>          (Justin A. Lemkul)
>       7. analysis using Gromacs tools  (oguz gurbulak)
> 
> 
>     ----------------------------------------------------------------------
> 
>     Message: 1
>     Date: Mon, 23 Feb 2009 06:37:30 -0800
>     From: akalabya bissoyi <bissoyi.akalabya at gmail.com
>     <mailto:bissoyi.akalabya at gmail.com>>
>     Subject: [gmx-users] gromac running in ubantu 8.10
>     To: gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>, gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     Message-ID:
>            <f166b2e50902230637i10031f2ck2e89ce4ef457a161 at mail.gmail.com
>     <mailto:f166b2e50902230637i10031f2ck2e89ce4ef457a161 at mail.gmail.com>>
>     Content-Type: text/plain; charset="iso-8859-1"
> 
>     hello everybody
> 
>     i have install gromac in my ubantu8.10 through synaptic package but
>     after
>     install how to run the programme, where to put the input file ,how
>     to run
>     the programme.
>     plz anybody help me.
>      thank u have nice day
> 
>     --
>     akalabya
>     N.I.T.Rourkela
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> 
>     ------------------------------
> 
>     Message: 2
>     Date: Mon, 23 Feb 2009 09:41:08 -0500
>     From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] gromac running in ubantu 8.10
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <49A2B584.60605 at vt.edu <mailto:49A2B584.60605 at vt.edu>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
>     akalabya bissoyi wrote:
>      > hello everybody
>      >
>      > i have install gromac in my ubantu8.10 through synaptic package but
>      > after install how to run the programme, where to put the input
>     file ,how
>      > to run the programme.
> 
>     1. Read the manual.
>     2. Search Google for "Gromacs tutorial"
>     3. Visit wiki.gromacs.org <http://wiki.gromacs.org> and read the
>     tutorial information and FAQ's there
> 
>     -Justin
> 
>      > plz anybody help me.
>      >  thank u have nice day
>      >
>      > --
>      > akalabya
>      > N.I.T.Rourkela
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      >
>      > _______________________________________________
>      > gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      > Please search the archive at http://www.gromacs.org/search before
>     posting!
>      > Please don't post (un)subscribe requests to the list. Use the
>      > www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
>     --
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 
>     ------------------------------
> 
>     Message: 3
>     Date: Mon, 23 Feb 2009 23:26:40 +0800
>     From: Lee Soin <nomadoro at gmail.com <mailto:nomadoro at gmail.com>>
>     Subject: [gmx-users] Turning off electrostatic or Van der Waals
>            interactions
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID:
>            <e2838e4e0902230726u4f3ffdbavea1e35a307a3a729 at mail.gmail.com
>     <mailto:e2838e4e0902230726u4f3ffdbavea1e35a307a3a729 at mail.gmail.com>>
>     Content-Type: text/plain; charset="iso-8859-1"
> 
>     Hi!
>     Is there an option to turn off electrostatic or Van der Waals
>     interactions
>     in GROMACS?
> 
>     --
>     Sun Li
>     Department of Physics
>     Nanjing University, China
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> 
>     ------------------------------
> 
>     Message: 4
>     Date: Mon, 23 Feb 2009 10:29:12 -0500
>     From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
>            interactions
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <49A2C0C8.4050104 at vt.edu <mailto:49A2C0C8.4050104 at vt.edu>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
>     Lee Soin wrote:
>      > Hi!
>      > Is there an option to turn off electrostatic or Van der Waals
>      > interactions in GROMACS?
>      >
> 
>     Look into the free energy code; if this is not your intent, be more
>     specific
>     with what you are trying to do.
> 
>     -Justin
> 
>      > --
>      > Sun Li
>      > Department of Physics
>      > Nanjing University, China
>      >
>      >
>      >
>     ------------------------------------------------------------------------
>      >
>      > _______________________________________________
>      > gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      > Please search the archive at http://www.gromacs.org/search before
>     posting!
>      > Please don't post (un)subscribe requests to the list. Use the
>      > www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
>     --
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 
>     ------------------------------
> 
>     Message: 5
>     Date: Mon, 23 Feb 2009 23:44:04 +0800
>     From: Lee Soin <nomadoro at gmail.com <mailto:nomadoro at gmail.com>>
>     Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
>            interactions
>     To: jalemkul at vt.edu <mailto:jalemkul at vt.edu>, Discussion list for
>     GROMACS users
>            <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>     Message-ID:
>            <e2838e4e0902230744i217553c3o6121a0aabd6228c0 at mail.gmail.com
>     <mailto:e2838e4e0902230744i217553c3o6121a0aabd6228c0 at mail.gmail.com>>
>     Content-Type: text/plain; charset="iso-8859-1"
> 
>     I'm trying to rule out the effect of electrostatic or Van der Waals
>     interactions while performing a simulation. Do you mean that I
>     should modify
>     the code and re-compile?
> 
>     2009/2/23 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
>      >
>      >
>      > Lee Soin wrote:
>      >
>      >> Hi!
>      >> Is there an option to turn off electrostatic or Van der Waals
>     interactions
>      >> in GROMACS?
>      >>
>      >>
>      > Look into the free energy code; if this is not your intent, be more
>      > specific with what you are trying to do.
>      >
>      > -Justin
>      >
>      >  --
>      >> Sun Li
>      >> Department of Physics
>      >> Nanjing University, China
>      >>
>      >>
>      >>
>     ------------------------------------------------------------------------
>      >>
>      >> _______________________________________________
>      >> gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      >> http://www.gromacs.org/mailman/listinfo/gmx-users
>      >> Please search the archive at http://www.gromacs.org/search before
>      >> posting!
>      >> Please don't post (un)subscribe requests to the list. Use the www
>      >> interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>      >>
>      >
>      > --
>      > ========================================
>      >
>      > Justin A. Lemkul
>      > Graduate Research Assistant
>      > Department of Biochemistry
>      > Virginia Tech
>      > Blacksburg, VA
>      > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>      > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >
>      > ========================================
>      > _______________________________________________
>      > gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      > http://www.gromacs.org/mailman/listinfo/gmx-users
>      > Please search the archive at http://www.gromacs.org/search before
>     posting!
>      > Please don't post (un)subscribe requests to the list. Use the www
>     interface
>      > or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>      > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>      >
> 
> 
> 
>     --
>     Sun Li
>     Department of Physics
>     Nanjing University, China
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>     ------------------------------
> 
>     Message: 6
>     Date: Mon, 23 Feb 2009 10:48:06 -0500
>     From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] Turning off electrostatic or Van der   Waals
>            interactions
>     To: "Gromacs Users' List" <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <49A2C536.6020308 at vt.edu <mailto:49A2C536.6020308 at vt.edu>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
>     Lee Soin wrote:
>      > I'm trying to rule out the effect of electrostatic or Van der Waals
>      > interactions while performing a simulation. Do you mean that I should
>      > modify the code and re-compile?
>      >
> 
>     No, I mean use the free energy options in the .mdp file.  You may be
>     able to use
>     a B-state in the topology with dummy atoms to accomplish what you
>     want to do.
> 
>     -Justin
> 
>      > 2009/2/23 Justin A. Lemkul <jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>     <mailto:jalemkul at vt.edu>>>
>      >
>      >
>      >
>      >     Lee Soin wrote:
>      >
>      >         Hi!
>      >         Is there an option to turn off electrostatic or Van der Waals
>      >         interactions in GROMACS?
>      >
>      >
>      >     Look into the free energy code; if this is not your intent,
>     be more
>      >     specific with what you are trying to do.
>      >
>      >     -Justin
>      >
>      >         --
>      >         Sun Li
>      >         Department of Physics
>      >         Nanjing University, China
>      >
>      >
>      >        
>     ------------------------------------------------------------------------
>      >
>      >         _______________________________________________
>      >         gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      >         <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>      >         http://www.gromacs.org/mailman/listinfo/gmx-users
>      >         Please search the archive at http://www.gromacs.org/search
>      >         before posting!
>      >         Please don't post (un)subscribe requests to the list. Use the
>      >         www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>
>      >         <mailto:gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>>.
>      >         Can't post? Read
>     http://www.gromacs.org/mailing_lists/users.php
>      >
>      >
>      >     --
>      >     ========================================
>      >
>      >     Justin A. Lemkul
>      >     Graduate Research Assistant
>      >     Department of Biochemistry
>      >     Virginia Tech
>      >     Blacksburg, VA
>      >     jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu/> | (540)
>     231-9080
>      >     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>      >
>      >     ========================================
>      >     _______________________________________________
>      >     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>      >     <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>      >     http://www.gromacs.org/mailman/listinfo/gmx-users
>      >     Please search the archive at http://www.gromacs.org/search before
>      >     posting!
>      >     Please don't post (un)subscribe requests to the list. Use the www
>      >     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>
>      >     <mailto:gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>>.
>      >     Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>      >
>      >
>      >
>      >
>      > --
>      > Sun Li
>      > Department of Physics
>      > Nanjing University, China
> 
>     --
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
> 
> 
>     ------------------------------
> 
>     Message: 7
>     Date: Mon, 23 Feb 2009 13:10:17 -0800 (PST)
>     From: oguz gurbulak <gurbulakoguz at yahoo.com
>     <mailto:gurbulakoguz at yahoo.com>>
>     Subject: [gmx-users] analysis using Gromacs tools
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Message-ID: <447025.52293.qm at web36301.mail.mud.yahoo.com
>     <mailto:447025.52293.qm at web36301.mail.mud.yahoo.com>>
>     Content-Type: text/plain; charset="utf-8"
> 
>     Dear All,
>     Â 
>     I'm planning to use Gromacs  for analysis with Amber trajectory
>     files ( mdcrd, rst files ). And I found a script that converts Amber
>     mdcrd files to Gromacs-compatible .xtc files. I want to learn that
>     if Gromacs-compatible .xtc files are enough to perform an analysis
>     using Gromacs tools ? or Will I have to have some other files for
>     analysis in Gromacs ?  I’m waiting for your suggestions and helps.
>     Â 
>     Thank you very much for your attention.
>     Â 
>     Sincerely
> 
> 
> 
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>     ------------------------------
> 
>     _______________________________________________
>     gmx-users mailing list
>     gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     http://www.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at http://www.gromacs.org/search before
>     posting!
> 
>     End of gmx-users Digest, Vol 58, Issue 125
>     ******************************************
> 
> 
> 
> 
> -- 
> akalabya
> N.I.T.Rourkela
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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