Hi Jamal,
the tutorials are probably for an amber version prior to the one you
have. TI is done a bit different now compared to the way the tutorials
describe. There might be a new tutorial on TI coming up in the near
future.
You no longer need a perturbed prmtop file, but you rather need
to have two 'normal' prmtops that correspond to your TI start- and
endstate. You would then run sander using two groups and the two processes
will communicate and figure out dvdl among each other. So what you need to
run is something like:
mpirun sander.MPI -ng 2 -groupfile <your_groupfile>
and <your_groupfile> will look like:
-------
-O -i mdin -p prmtop_startstate -o mdout.0 -c ...
-O -i mdin -p prmtop_endstate -o mdout.1 -c ...
-------
mdin will contain your clambda, icfe and klambda keywords.
Most output should be identical from both processes and both will contain
the dvdl that you need to proceed. Chapter 6.5 of the amber manual will
give you more details.
Kind regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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Received on Sun May 20 2007 - 06:07:08 PDT
