[gmx-users] g-hbond -sel problem
feenstra at few.vu.nl
Fri Jun 17 11:21:20 CEST 2005
Henrik Rundgren wrote:
> I have tried to use the -sel command. Both using the beta and the 3.2.1
> The problem that I get is that when using -sel and an index file
> (originating from the command -hbn), I get NO hbonds at all.
> But when using the -n command instead I get hbonds.
> So, is there still a bug?
> To check, I understand that when using -sel I would get a outfile where
> I can see each individual hbond by itself (one coloumn per group in the
> index file in the outfile?) and not as a group. Or would I still need o
> run the program on each individual? If the later, then it works with -n
> command, and it's just to rerun it the needed times. and that we can
> script ofcourse...
-sel is meant to work by taking triplets of atoms (D-H-A, iirc) from
*one* index group, and produce, indeed as you say, output for each
individual hbond. Some output would still be summed or averaged over all
hbonds, though. (But, it's been a while since I last used it...)
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