[gmx-users] H-bond analysis

2018-10-10 Thread Valerio Ferrario 
Dear all,

I would like to calculate the water residence time for specific protein
residues...

Therefore I created an index file and used gmx hbonds using the -ac option

Every time I have segmentation fault at the beginning of the ac calculation
(the calculation of the number of H-bonds is fine).

I have also tried to calculate just the number and perform the calculation
with gmx analyze using the -luzar option but again I have segmentation
fault...

Can anyone tell me if I am doing something wrong and how to follow the
right procedure?

Thanks a lot in avvance.

Valerio Ferrario
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[gmx-users] H-bond analysis

2014-04-17 Thread michael.b 

hi,

I try to analyze H-bonds in an MD trajectory.
when i look at the definition of an H-bond used by g_hbond it appears
that only three atoms (acceptor, donor, hydrogen, ADH) are used
in the analysis performed by this program ... however, i would assume that
in fact 4 (or up to 6) atoms should be considered because the existence and
the strength of an H-bond not only depend on the A-D distance and
the ADH angle  but also on the orientation of the lone pairs of the
acceptor, and the latter are actually determined by the geometry of
the atom(s), call them X, the acceptor is covalently bound to, aren't they?

So, in short, my question is: is anybody aware of a tool that
can analyze the H-bonds in MD trajectories considering not only
A-D distance and ADH angle but also the position of X (basically
the dihedral DHAX) ?

thanks for any hints
cheers,
michael




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