hello everybody<br>
thank you for u suggestion, as i am new to Linux. so i am facing problem in find out my working directory.<br>what is the universal path location of gromac in ubantu 8.10 where i can type my command for execute the programme.<br>
plz help me regarding finding working directory.<br><br><div class="gmail_quote">On Tue, Feb 24, 2009 at 2:41 AM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Send gmx-users mailing list submissions to<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:gmx-users-owner@gromacs.org">gmx-users-owner@gromacs.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of gmx-users digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. gromac running in ubantu 8.10 (akalabya bissoyi)<br>
2. Re: gromac running in ubantu 8.10 (Justin A. Lemkul)<br>
3. Turning off electrostatic or Van der Waals interactions (Lee Soin)<br>
4. Re: Turning off electrostatic or Van der Waals interactions<br>
(Justin A. Lemkul)<br>
5. Re: Turning off electrostatic or Van der Waals interactions<br>
(Lee Soin)<br>
6. Re: Turning off electrostatic or Van der Waals interactions<br>
(Justin A. Lemkul)<br>
7. analysis using Gromacs tools (oguz gurbulak)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Mon, 23 Feb 2009 06:37:30 -0800<br>
From: akalabya bissoyi <<a href="mailto:bissoyi.akalabya@gmail.com">bissoyi.akalabya@gmail.com</a>><br>
Subject: [gmx-users] gromac running in ubantu 8.10<br>
To: <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>, <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:f166b2e50902230637i10031f2ck2e89ce4ef457a161@mail.gmail.com">f166b2e50902230637i10031f2ck2e89ce4ef457a161@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
hello everybody<br>
<br>
i have install gromac in my ubantu8.10 through synaptic package but after<br>
install how to run the programme, where to put the input file ,how to run<br>
the programme.<br>
plz anybody help me.<br>
thank u have nice day<br>
<br>
--<br>
akalabya<br>
N.I.T.Rourkela<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/15c5dae0/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/15c5dae0/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Mon, 23 Feb 2009 09:41:08 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] gromac running in ubantu 8.10<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:49A2B584.60605@vt.edu">49A2B584.60605@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
akalabya bissoyi wrote:<br>
> hello everybody<br>
><br>
> i have install gromac in my ubantu8.10 through synaptic package but<br>
> after install how to run the programme, where to put the input file ,how<br>
> to run the programme.<br>
<br>
1. Read the manual.<br>
2. Search Google for "Gromacs tutorial"<br>
3. Visit <a href="http://wiki.gromacs.org" target="_blank">wiki.gromacs.org</a> and read the tutorial information and FAQ's there<br>
<br>
-Justin<br>
<br>
> plz anybody help me.<br>
> thank u have nice day<br>
><br>
> --<br>
> akalabya<br>
> N.I.T.Rourkela<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Mon, 23 Feb 2009 23:26:40 +0800<br>
From: Lee Soin <<a href="mailto:nomadoro@gmail.com">nomadoro@gmail.com</a>><br>
Subject: [gmx-users] Turning off electrostatic or Van der Waals<br>
interactions<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:e2838e4e0902230726u4f3ffdbavea1e35a307a3a729@mail.gmail.com">e2838e4e0902230726u4f3ffdbavea1e35a307a3a729@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi!<br>
Is there an option to turn off electrostatic or Van der Waals interactions<br>
in GROMACS?<br>
<br>
--<br>
Sun Li<br>
Department of Physics<br>
Nanjing University, China<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/b8f40279/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/b8f40279/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Mon, 23 Feb 2009 10:29:12 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals<br>
interactions<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:49A2C0C8.4050104@vt.edu">49A2C0C8.4050104@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Lee Soin wrote:<br>
> Hi!<br>
> Is there an option to turn off electrostatic or Van der Waals<br>
> interactions in GROMACS?<br>
><br>
<br>
Look into the free energy code; if this is not your intent, be more specific<br>
with what you are trying to do.<br>
<br>
-Justin<br>
<br>
> --<br>
> Sun Li<br>
> Department of Physics<br>
> Nanjing University, China<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Mon, 23 Feb 2009 23:44:04 +0800<br>
From: Lee Soin <<a href="mailto:nomadoro@gmail.com">nomadoro@gmail.com</a>><br>
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals<br>
interactions<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<<a href="mailto:e2838e4e0902230744i217553c3o6121a0aabd6228c0@mail.gmail.com">e2838e4e0902230744i217553c3o6121a0aabd6228c0@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
I'm trying to rule out the effect of electrostatic or Van der Waals<br>
interactions while performing a simulation. Do you mean that I should modify<br>
the code and re-compile?<br>
<br>
2009/2/23 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
<br>
><br>
><br>
> Lee Soin wrote:<br>
><br>
>> Hi!<br>
>> Is there an option to turn off electrostatic or Van der Waals interactions<br>
>> in GROMACS?<br>
>><br>
>><br>
> Look into the free energy code; if this is not your intent, be more<br>
> specific with what you are trying to do.<br>
><br>
> -Justin<br>
><br>
> --<br>
>> Sun Li<br>
>> Department of Physics<br>
>> Nanjing University, China<br>
>><br>
>><br>
>> ------------------------------------------------------------------------<br>
>><br>
>> _______________________________________________<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
>> posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the www<br>
>> interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
>><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Graduate Research Assistant<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www interface<br>
> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
<br>
<br>
<br>
--<br>
Sun Li<br>
Department of Physics<br>
Nanjing University, China<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/23e209f2/attachment-0001.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/23e209f2/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Mon, 23 Feb 2009 10:48:06 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals<br>
interactions<br>
To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:49A2C536.6020308@vt.edu">49A2C536.6020308@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
Lee Soin wrote:<br>
> I'm trying to rule out the effect of electrostatic or Van der Waals<br>
> interactions while performing a simulation. Do you mean that I should<br>
> modify the code and re-compile?<br>
><br>
<br>
No, I mean use the free energy options in the .mdp file. You may be able to use<br>
a B-state in the topology with dummy atoms to accomplish what you want to do.<br>
<br>
-Justin<br>
<br>
> 2009/2/23 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>>><br>
><br>
><br>
><br>
> Lee Soin wrote:<br>
><br>
> Hi!<br>
> Is there an option to turn off electrostatic or Van der Waals<br>
> interactions in GROMACS?<br>
><br>
><br>
> Look into the free energy code; if this is not your intent, be more<br>
> specific with what you are trying to do.<br>
><br>
> -Justin<br>
><br>
> --<br>
> Sun Li<br>
> Department of Physics<br>
> Nanjing University, China<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Graduate Research Assistant<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu/" target="_blank">http://vt.edu/</a>> | (540) 231-9080<br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> _______________________________________________<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
> posting!<br>
> Please don't post (un)subscribe requests to the list. Use the www<br>
> interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a><br>
> <mailto:<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
><br>
><br>
><br>
><br>
> --<br>
> Sun Li<br>
> Department of Physics<br>
> Nanjing University, China<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 7<br>
Date: Mon, 23 Feb 2009 13:10:17 -0800 (PST)<br>
From: oguz gurbulak <<a href="mailto:gurbulakoguz@yahoo.com">gurbulakoguz@yahoo.com</a>><br>
Subject: [gmx-users] analysis using Gromacs tools<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:447025.52293.qm@web36301.mail.mud.yahoo.com">447025.52293.qm@web36301.mail.mud.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear All,<br>
 <br>
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.<br>
 <br>
Thank you very much for your attention.<br>
 <br>
Sincerely<br>
<br>
<br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/2d2ac454/attachment.html" target="_blank">http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/2d2ac454/attachment.html</a><br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
gmx-users mailing list<br>
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
<br>
End of gmx-users Digest, Vol 58, Issue 125<br>
******************************************<br>
</blockquote></div><br><br clear="all"><br>-- <br>akalabya<br>N.I.T.Rourkela<br>