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

[Erik Marklund]

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
>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/