[gmx-users] Re: [Fwd: query]
k.a.feenstra at chem.rug.nl
Mon Jan 7 09:27:37 CET 2002
From the information you supply, I cannot tell what you are doing wrong.
Anyway, your best bet for these type of questions is the Gromacs users
mailing list (gmx-users at gromacs.org). That way, many more people will
read your question, which increases the chances of getting a quick, and
helpful, reply. You must be subscribed to the list to be allowed to send
messages to it. You can subscribe on-line at www.gromacs.org.
Also, I noticed you are still using Gromacs 2.0. I would strongly suggest
you upgrade to 3.0. 2.0 is no longer supported, and 3.0 has many new and
enhanced features, and is also generally more user-friendly. Not the least
important is, that on many types of hardware it is considerably faster,
up to a factor of more than two (!) on Intel/AMD platforms!
> -------- Original Message --------
> Subject: query
> From: "Seema Namboori" <docs2n at rediffmail.com>
> Hello ,
> I am a student of Indian Institute of Technology,Bombay
> I am using Gromacs 2.0 I would like to know as to how am i supposed to
> use the "g_hbond" tool to analyze the 'hydrogen bond distance' between
> specific groups of atoms?
> I have already manually made an index file of donor-hydrogen-acceptor
> atoms.But somehow i am unable to get the hydrogen bond distances between
> the specific groups that i am interested.What i am unable to understand
> is exactly what options (i know that '-sel' is one of the options) am i
> to give for me to get the Hbond distance?
> I want to plot the 'Hbond distance against time' and i did not realize,
> even after repeated attempt,the output option for what i want.
> It would be great help if u could enlightn me in this regard.
> Dr Seema Namboori
| | Anton Feenstra Dept. of Biophysical Chemistry |
| _ _ ___,| K.A.Feenstra at chem.rug.nl University of Groningen |
| / \ / \'| | | Tel +31 50 363 4327 Nijenborgh 4 |
|( | )| | | Fax +31 50 363 4800 9747 AG Groningen |
| \_/ \_/ | | | http://md.chem.rug.nl/~anton The Netherlands |
| | "As Always Your Logic Is Impeccable" (Tuvok) |
More information about the gromacs.org_gmx-users