[gmx-users] query regarding replica exchange

Sanku M msanku65 at yahoo.com
Wed May 25 20:50:00 CEST 2011


  I am planning to run replica exchange simulation using gromacs 4.0.7 . I have 
read the manual about REMD. Only thing I wanted to know is that how I can 
specify the name of host-machines where I am planning to run the simulations. 

I have 10 different quad-core computers each intra-connected with the other each 
running OPENMPI. I want to run 20 replica each using 2 cores in parallel.

So, I was wondering whether I have to create any file containing the names of 
those machines . If so, can someone give an example of format of the file which 
contain those names ? Finally, what keyword I should use in mdrun to specify 
that file for running replica exchange. 

Also, I am not using any PBS for submitting jobs.

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