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.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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