[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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> 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!
> Please don't post (un)subscribe requests to the list. Use the
> 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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