Re: [AMBER] TI tutorial

From: David A Case <>
Date: Fri, 8 Nov 2013 07:09:10 -0500

On Thu, Nov 07, 2013, Terry M. Gray wrote:

> I'm working through the free energy tutorial with benzene, phenol,
> T4Lysozyme cavity mutant.
> I notice that the sample script included is set up to use mpi and the
> group option with sander.MPI. Is there a reason this has to be done
> parallel?

To carry out TI, sander.MPI creates two threads: one to compute V0, the other
to compute V1. Forces are then constructed from a mixture of the the forces
in the two end states.

So yes, you need to have a parallel installation. It's not hard: go to the
AmberTools/src directory and run the configure_mpich2 script (you'll have to
download some files). This should set up everything correctly, with the
proper paths and so on.


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Received on Fri Nov 08 2013 - 04:30:03 PST
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