[gmx-users] using xmp file

[Justin A. Lemkul]

Quoting pragya chohan <pragyachohan at hotmail.com>:

>
> 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: dommert at fias.uni-frankfurt.de>
> To: gmx-users at 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> >
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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/

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