[gmx-users] hydrogen bond lifetimes
Y U Sasidhar
sasidhar at chem.iitb.ac.in
Sat Aug 10 15:13:43 CEST 2002
There should also be a text file output from g_hbond which gives
information about hbonds.
Another way is to use g_dist to compute distance between ,say- NH of 5
th residue and CO of 1 st residue ( helix h bond ) and use the criterion
that d < 2.6 A for h bond. ( d < sum of vanderwalls radii ; O-1.4 A, H-
1.2 A ). g_dist will give output xvg file from which d as a function of
t can be processed to calculate life times etc. xmgrace can display this
Mikko Huhtala wrote:
> I am looking for a way to compute average and median lifetimes of
> particular hydrogen bonds in a trajectory. These values can be
> computed from the data in the hbmap.xpm file written by g_hbond, but
> the file is in a binary format and it is a bit awkward to parse. Am I
> missing something obvious or should I go ahead to cook something to
> extract the numbers from hbmap.xpm?
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