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
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
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 usersI 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
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 usersI 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
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
