[gmx-users] g-hbond -sel problem

[Anton Feenstra]

Henrik Rundgren wrote:

> Hi,
> I have tried to use the -sel command. Both using the beta and the 3.2.1 
> version.
> 
> 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...)


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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