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

[Erik Marklund]

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.

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
>>
>>
>
>


-- 
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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