[gmx-users] gromacs (fwd)

David van der Spoel spoel at xray.bmc.uu.se
Tue Jul 5 20:40:39 CEST 2005

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

---------- Forwarded message ----------
Date: Mon, 27 Jun 2005 14:54:15 +0430
From: amininasab <amininasab at ibb.ut.ac.ir>
To: spoel at xray.bmc.uu.se
Subject: gromacs

Dear Prof. Spoel,

I have a problem with gromacs. I would like to analyze hydrogen bonds 
over the trajectory of my protein using gromacs 3.2.1 especially 
identifying donor,hydrogen and acceptor and hydrogen bond lifetime.
In gromacs 3.2.1 I applied the following command:
 g_hbond -f traj.trr -s prot.tpr -hx -hbn -g -num -ac 

I think something is wrong because in the hbond.ndx we can see the donor 
and aceptor groups but there is nothing about the atoms in hydroge bond. 
In hbnum the number of hydrogen bonds is computed and listed.
In hbond.log there is only one title line and nothing is present about 
hydrogen bonds. I don't know what is the problem and how I can solve it.
Also I would like to know how can I compute the lifetimes of hydrogen 
looking forward your early reply.

sincerely yours,
Mehriar Amininasab,PhD
Inst. of Biochem. & Biophys.,
P.O. Box 13145-1384,
Univ. of Tehran,

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