[gmx-users] Replica exchange questions

[Xavier Periole]

Marc Baaden wrote:

>Hi,
>
>we are planning to use replica exchange very soon on a rather big system.
>  
>
I do not know what is your plan but my experience indicates that REMD on 
big system
may not be very usefull. It will alway increase the sampling enormously, 
compared to normal
MD, but if you plan to fold a big thing that migh not be helping much. 
Depends on your plans
of course.

>What is the current state in Gromacs ? Eg:
>
>* which Gromacs version is recommended for replica exchange, 3.3 or CVS or some 
>  custom version ?
>  
>
there is a version that I know and 've been using running the 3.1.4, 
from Walter and Luca in Calgary.
It is probably bug free. And the CVS version that I know runs. I tried 
but never checked for bugs.

>* are there known bugs/shortcomings ?
>  
>
not that I know.

>* can the individual replicas be parallelized ? Eg could one run 20 replicas, each
>  using 16 procs or can a replica only run on a single CPU ?
>  
>
Not that I know but will need a version like you describe pretty soon 
and I'd be interested in
helping.

>* are there any RE tutorials for gromacs ?
>  
>
Not that I know.

>Thanks in advance,
>  Marc Baaden
>
>  
>
Best
XAvier

-- 
----------------------------------
 Xavier Periole - Ph.D.

 Dept. of Biophysical Chemistry / MD Group   
 Univ. of Groningen
 Nijenborgh 4
 9747 AG Groningen
 The Netherlands
 
 Tel: +31-503634329
 Fax: +31-503634800
 email: x.periole at rug.nl
 web-page: http://md.chem.rug.nl/~periole
----------------------------------