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
[email protected] http://folding.bmc.uu.se/
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