[gmx-users] Re: coarse grain hydrogen bonding

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 2 20:37:53 CEST 2011

Tsjerk's message covered this:


To detect a hydrogen bond in a conventional sense using geometric criteria, you 
need an atomistic representation.  There are tools available to reconstruct 
atomic positions from CG models, but I have never used them so I will not 
comment further other than to suggest you may want to investigate them.  Of 
course, that leaves open for debate whether or not the hydrogen bond would 
actually be there or if it is caused solely by the reconstruction algorithm.

My sense is that no, there isn't a very easy way to collect hydrogen bonding 
data from a CG trajectory.


Sara baretller wrote:
> Hi Justin you mentioned in the past email that i can not use the measure 
> hbond;
> do you suggest any other way to find the hbond??
> thank you


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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