Got the TI tutorial running. Thanks for your help.
TG
On Fri, Nov 8, 2013 at 5:09 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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.
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Terry M. Gray, Ph.D.
Instructor, Colorado State University
Research Associate, Colorado State University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 08 2013 - 15:30:02 PST
