[gmx-users] Re: [Fwd: query]

[K.A.Feenstra]

Dear Seema,


 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.
> 
> Thanks,
> Dr Seema Namboori

-- 
Groetjes,

Anton
 _____________ _____________________________________________________
|             | 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)        |
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