Re: [gmx-users] using xmp file
pragya chohan wrote: Hi i found out the residues which form H bond but am still not able to get life time if H bond. The option -lifetime gives t as x and p(t) as y axis. is this value for all the bonds. How can i see the lifetime of each bond? There's an option for this. You can learn about it the same way I did - read "g_hbond -h" Mark ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] using xmp file
Quoting pragya chohan <[EMAIL PROTECTED]>: > > Hi > i found out the residues which form H bond but am still not able to get life > time if H bond. The option -lifetime gives t as x and p(t) as y axis. is this > value for all the bonds. > How can i see the lifetime of each bond? I suppose that, if you've identified the residues involved in H-bonding, you could create index groups for these residues and feed the index groups into g_hbond. This is the case with most (if not all) Gromacs tools. -Justin > > Thanking you > > pragya chohan > > Date: Sat, 3 May 2008 02:06:52 +0200> From: [EMAIL PROTECTED]> > To: gmx-users@gromacs.org> Subject: Re: [gmx-users] using xmp file> > Mark > Abraham wrote:> > pragya chohan wrote:> >> Dear users> >> > >> I wasted to > look at H bonding between between a particular residue> >> and rest of the > system. So I did g_hbond. It created a number of> >> files I want to make a > table indicating atom of residue> >> participating, atom or residue number of > Donor atom, lifetime of> >> those bonds to show their significance.> >> > >> > Can you tell me which files are useful for this purpose? > >> > Yes, but > first you should be reading "g_hbond -h" and working some> > things out for > yourself.> >> >> Also please tell me how to visualise xmp files on windows>> > >> > Google is probably your friend for finding out about viewers for *xpm*> > > files. The GIMP will certainly work, but it's a heavyweight solution!> >> > Perhaps the xpm2ps tool will also help to view a ps document, which> should > be possible with windows ;)> > > > Mark> > > ___> > 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 [EMAIL PROTECTED]> > Can't post? > Read http://www.gromacs.org/mailing_lists/users.php> >> > > -- > Florian > Dommert> Dipl.-Phys.> > Computational and Theoretical Softmatter & Biophysics > group> > Frankfurt Institute for Advanced Studies> Johann-Wolfgang-Goethe > University> > Ruth-Moufang-Str. 1> 60438 Frankfurt am Main> > Phone: +49(0)69 > / 798 - 47522> Fax: +49(0)69 / 798 - 47611> > EMail: > [EMAIL PROTECTED]> Home: > http://fias.uni-frankfurt.de/~simbio/Florian_Dommert> > _ > Watch hottest Bollywood videos, clips, movie tailors, star interviews, songs > and more on MSN videos. > http://video.msn.com/?mkt=en-in Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] using xmp file
Hi i found out the residues which form H bond but am still not able to get life time if H bond. The option -lifetime gives t as x and p(t) as y axis. is this value for all the bonds. How can i see the lifetime of each bond? Thanking you pragya chohan > Date: Sat, 3 May 2008 02:06:52 +0200> From: [EMAIL PROTECTED]> To: > gmx-users@gromacs.org> Subject: Re: [gmx-users] using xmp file> > Mark > Abraham wrote:> > pragya chohan wrote:> >> Dear users> >> > >> I wasted to > look at H bonding between between a particular residue> >> and rest of the > system. So I did g_hbond. It created a number of> >> files I want to make a > table indicating atom of residue> >> participating, atom or residue number of > Donor atom, lifetime of> >> those bonds to show their significance.> >> > >> > Can you tell me which files are useful for this purpose? > >> > Yes, but > first you should be reading "g_hbond -h" and working some> > things out for > yourself.> >> >> Also please tell me how to visualise xmp files on windows>> > >> > Google is probably your friend for finding out about viewers for *xpm*> > > files. The GIMP will certainly work, but it's a heavyweight solution!> >> > Perhaps the xpm2ps tool will also help to view a ps document, which> should > be possible with windows ;)> > > > Mark> > > ___> > 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 [EMAIL PROTECTED]> > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php> >> > > -- > Florian Dommert> > Dipl.-Phys.> > Computational and Theoretical Softmatter & Biophysics group> > > Frankfurt Institute for Advanced Studies> Johann-Wolfgang-Goethe University> > > Ruth-Moufang-Str. 1> 60438 Frankfurt am Main> > Phone: +49(0)69 / 798 - > 47522> Fax: +49(0)69 / 798 - 47611> > EMail: [EMAIL PROTECTED]> Home: > http://fias.uni-frankfurt.de/~simbio/Florian_Dommert> _ Watch hottest Bollywood videos, clips, movie tailors, star interviews, songs and more on MSN videos. http://video.msn.com/?mkt=en-in___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using xmp file
Mark Abraham wrote: > pragya chohan wrote: >> Dear users >> >> I wasted to look at H bonding between between a particular residue >> and rest of the system. So I did g_hbond. It created a number of >> files I want to make a table indicating atom of residue >> participating, atom or residue number of Donor atom, lifetime of >> those bonds to show their significance. >> >> Can you tell me which files are useful for this purpose? > > Yes, but first you should be reading "g_hbond -h" and working some > things out for yourself. > >> Also please tell me how to visualise xmp files on windows> > > Google is probably your friend for finding out about viewers for *xpm* > files. The GIMP will certainly work, but it's a heavyweight solution! > Perhaps the xpm2ps tool will also help to view a ps document, which should be possible with windows ;) > Mark > ___ > gmx-users mailing listgmx-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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Florian Dommert Dipl.-Phys. Computational and Theoretical Softmatter & Biophysics group Frankfurt Institute for Advanced Studies Johann-Wolfgang-Goethe University Ruth-Moufang-Str. 1 60438 Frankfurt am Main Phone: +49(0)69 / 798 - 47522 Fax: +49(0)69 / 798 - 47611 EMail: [EMAIL PROTECTED] Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert begin:vcard fn:Florian Dommert n:Dommert;Florian email;internet:[EMAIL PROTECTED] x-mozilla-html:FALSE version:2.1 end:vcard signature.asc Description: OpenPGP digital signature ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] using xmp file
pragya chohan wrote: Dear users I wasted to look at H bonding between between a particular residue and rest of the system. So I did g_hbond. It created a number of files I want to make a table indicating atom of residue participating, atom or residue number of Donor atom, lifetime of those bonds to show their significance. Can you tell me which files are useful for this purpose? Yes, but first you should be reading "g_hbond -h" and working some things out for yourself. Also please tell me how to visualise xmp files on windows> Google is probably your friend for finding out about viewers for *xpm* files. The GIMP will certainly work, but it's a heavyweight solution! Mark ___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] using xmp file
Dear users I wasted to look at H bonding between between a particular residue and rest of the system. So I did g_hbond. It created a number of files I want to make a table indicating atom of residue participating, atom or residue number of Donor atom, lifetime of those bonds to show their significance. Can you tell me which files are useful for this purpose? Also please tell me how to visualise xmp files on windows> Thanking You Pragya Chohan _ 2000 Placements last year. Are You next ? Find out http://ss1.richmedia.in/recurl.asp?pid=499___ gmx-users mailing listgmx-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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php