[gmx-users] How to countting hydrogen bond lifetime and donor--acceptor residue's atom ?

Justin A. Lemkul jalemkul at vt.edu
Thu Feb 24 13:26:56 CET 2011

Erik Marklund wrote:
> Maybe I misunderstood. What you presented in a table is the hbond 
> occupancies, not the lifetimes. I beleve that Justin Lemkul once posted 
> a script for calculating occupancies.

The posted output is from my script, and it is indeed a simple percentage of 
times in which a given hydrogen bond occurs.  Hopefully the OP and others who 
have used it are not confusing occupancies and lifetimes.


> Erik
> Erik Marklund skrev 2011-02-24 13.15:
>> For now, use the kinetic model by Luzar and Chandler which is 
>> implemented in Gromacs. There's an implementation of the Geminate 
>> recombination model by Omer Markovitch underway, but it still has 
>> convergence problems that needs to be dealt with.
>> Erik
>> gromacs564 skrev 2011-02-24 13.11:
>>> Dear all
>>>    I want to count all of the hydrogen bond's lifetime and 
>>> donor-acceptor atoms in simulation,but I don't know how to do it.
>>> In many papers,the hydrogen bonds are list in this form:
>>> >     Donor                           
>>> Acceptor                            %Exist.
>>> >     ARG58           NH1       SOL2253            OW            21.663
>>> >     ARG58           NH1       SOL7338            OW            
>>> 0.160< BR>>     ARG58            NE       SOL3595             
>>> OW           1.359
>>> Can you give me some proposal?
>>> best regards


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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