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-requ...@gromacs.org> wrote: > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > 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> > Subject: [gmx-users] gromac running in ubantu 8.10 > To: gmx-users-requ...@gromacs.org, gmx-users@gromacs.org > Message-ID: > <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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/15c5dae0/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Mon, 23 Feb 2009 09:41:08 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] gromac running in ubantu 8.10 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <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 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 > > 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. > > 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 <nomad...@gmail.com> > Subject: [gmx-users] Turning off electrostatic or Van der Waals > interactions > To: gmx-users@gromacs.org > Message-ID: > <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 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/b8f40279/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Mon, 23 Feb 2009 10:29:12 -0500 > From: "Justin A. Lemkul" <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> > Message-ID: <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 > > 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. > > 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 <nomad...@gmail.com> > Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals > interactions > To: jalem...@vt.edu, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: > <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> > > > > > > > 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 > >> 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. > >> 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@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. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > Sun Li > Department of Physics > Nanjing University, China > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/23e209f2/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Mon, 23 Feb 2009 10:48:06 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Turning off electrostatic or Van der Waals > interactions > To: "Gromacs Users' List" <gmx-users@gromacs.org> > Message-ID: <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>> > > > > > > > > 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 > > -- > ======================================== > > 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 <gurbulako...@yahoo.com> > Subject: [gmx-users] analysis using Gromacs tools > To: gmx-users@gromacs.org > Message-ID: <447025.52293...@web36301.mail.mud.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, >  > 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. >  > Thank you very much for your attention. >  > Sincerely > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.gromacs.org/pipermail/gmx-users/attachments/20090223/2d2ac454/attachment.html > > ------------------------------ > > _______________________________________________ > gmx-users mailing list > gmx-users@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
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