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-requ...@gromacs.org
<mailto:gmx-users-requ...@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.akala...@gmail.com
<mailto:bissoyi.akala...@gmail.com>>
Subject: [gmx-users] gromac running in ubantu 8.10
To: gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>, gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
Message-ID:
<f166b2e50902230637i10031f2ck2e89ce4ef457a...@mail.gmail.com
<mailto:f166b2e50902230637i10031f2ck2e89ce4ef457a...@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" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] gromac running in ubantu 8.10
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <49a2b584.60...@vt.edu <mailto:49a2b584.60...@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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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 <nomad...@gmail.com <mailto:nomad...@gmail.com>>
Subject: [gmx-users] Turning off electrostatic or Van der Waals
interactions
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID:
<e2838e4e0902230726u4f3ffdbavea1e35a307a3a...@mail.gmail.com
<mailto:e2838e4e0902230726u4f3ffdbavea1e35a307a3a...@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" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
interactions
To: Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <49a2c0c8.4050...@vt.edu <mailto:49a2c0c8.4050...@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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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 <nomad...@gmail.com <mailto:nomad...@gmail.com>>
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
interactions
To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for
GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
Message-ID:
<e2838e4e0902230744i217553c3o6121a0aabd622...@mail.gmail.com
<mailto:e2838e4e0902230744i217553c3o6121a0aabd622...@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 <jalem...@vt.edu <mailto:jalem...@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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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@gromacs.org
<mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@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" <jalem...@vt.edu <mailto:jalem...@vt.edu>>
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals
interactions
To: "Gromacs Users' List" <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
Message-ID: <49a2c536.6020...@vt.edu <mailto:49a2c536.6020...@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 <jalem...@vt.edu
<mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
<mailto:jalem...@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@gromacs.org
<mailto:gmx-users@gromacs.org>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
> <mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@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@gromacs.org
<mailto:gmx-users@gromacs.org>
> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
> <mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@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 <gurbulako...@yahoo.com
<mailto:gurbulako...@yahoo.com>>
Subject: [gmx-users] analysis using Gromacs tools
To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
Message-ID: <447025.52293...@web36301.mail.mud.yahoo.com
<mailto:447025.52293...@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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--
========================================
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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