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

akalabya bissoyi bissoyi.akalabya at gmail.com
Tue Feb 24 02:51:16 CET 2009


hello everybody
thank you for u suggestion,  as i am new to Linux. so i am facing problem in
find out my working directory.
what is the universal path location of gromac in ubantu 8.10  where i can
type my command for execute the programme.
plz help me regarding finding working directory.

On Tue, Feb 24, 2009 at 2:41 AM, <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>
> Subject: [gmx-users] gromac running in ubantu 8.10
> To: gmx-users-request at gromacs.org, gmx-users at gromacs.org
> Message-ID:
>        <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>
> Subject: Re: [gmx-users] gromac running in ubantu 8.10
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <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 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
> > 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 23 Feb 2009 23:26:40 +0800
> From: Lee Soin <nomadoro at gmail.com>
> Subject: [gmx-users] Turning off electrostatic or Van der Waals
>        interactions
> To: gmx-users at gromacs.org
> Message-ID:
>        <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>
> Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
>        interactions
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <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
> > 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 23 Feb 2009 23:44:04 +0800
> From: Lee Soin <nomadoro at gmail.com>
> Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
>        interactions
> To: jalemkul at vt.edu, Discussion list for GROMACS users
>        <gmx-users at gromacs.org>
> Message-ID:
>        <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>
>
> >
> >
> > 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
> >> 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
> >
> > ========================================
> > _______________________________________________
> > 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
> >
>
>
>
> --
> 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>
> Subject: Re: [gmx-users] Turning off electrostatic or Van der   Waals
>        interactions
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <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>>
> >
> >
> >
> >     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
>
> --
> ========================================
>
> 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 7
> Date: Mon, 23 Feb 2009 13:10:17 -0800 (PST)
> From: oguz gurbulak <gurbulakoguz at yahoo.com>
> Subject: [gmx-users] analysis using Gromacs tools
> To: gmx-users at gromacs.org
> Message-ID: <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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> End of gmx-users Digest, Vol 58, Issue 125
> ******************************************
>



-- 
akalabya
N.I.T.Rourkela
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