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 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
