[gmx-developers] Implementation of H-bond analysis

[Mark Abraham]

Emanuel Peter wrote:
> Quoting Anton Feenstra <feenstra at few.vu.nl>:
> 
>> Erik Marklund wrote:
>>> Hi,
>>>
>>> I second that. What you intend to do sounds much easier to
>> implement in
>>> g_hbond.
>> Yes, exactly my point. If you need 'more frequent H-bond analysis',
>> just
>> write more frames to your trajectory and use g_hbond (100 steps is .2
>> ps). No use in burdening mdrun with this.
>>
>> Unless, of course, Emanual really want to add some sort of
>> interaction
>> to the H-bonds. Emanuel can you clarify this?
>>
>>
>> --
>> Groetjes,
>>
>> Anton
>>   _____________
>> _______________________________________________________
>> |             |
>> |
>> |  _   _  ___,| K. Anton Feenstra
>> |
>> | / \ / \'| | | IBIVU/Bioinformatics - Free University  Amsterdam
>> |
>> |(   |   )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands
>> |
>> | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136
>> |
>> |             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/
>> |
>> |             | "You Could Be a Shadow" (The Breeders)
>> |
>>
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> 
> 
> Dear Developers,
> 
> My intention is to make use of a hydrogen-donor-acceptor list in a new
> algorithm that follows after the nth-MD-step.

Sure, but the question is whether you need to *use* the result for a 
subsequent MD step, or only after the simulation is done. If the former, 
then you need to modify mdrun, if the latter, you don't.

> This algorithm needs the last coordinate-conformation and a list of
> temporarily existing H-bonds.
> Analysing just the H-bonds from the trajectory .trr or .xtc is not my
> problem.

Mark