amber-developers: new method for free energy calculations in Amber 9

From: David A. Case <>
Date: Wed, 29 Jun 2005 13:44:37 -0700


I have turned on some new code in Amber 9 for doing free energy
with thermodynamic integration.

The new method uses multisander to run two groups (each group itself have
several cpu's). The first group computes the lambda=0 energy and forces,
the second group computes the same for lambda=1. There is no longer any
for a "pert" prmtop file: each group reads a regular prmtop corresponding
one of the endpoints.

Then, at each step, the energies and forces and communicated and combined
to give the actualy Hamiltonian.

The advantage is that there is no need for a perturbed prmtop file, which
should eliminate lots of confusion. You just create two prmtop files for
endpoints (which you can test and interrogate in the usual way). When you
satisfied with the endpoints, you can compute the free energy difference
between them. Also, there is more flexibility about choosing the states,
since the current code has only a single bond-list for both states. This
means that you cannot convert a 1-3 interaction (say) into a 1-4
in any simple fashion.

The two prmtop files *must* have the same number of atoms in the same
the coordinates on the two processes are kept synchronized. Also, a minor
disadvantage is that you must be running MPI to do free energy
But I think the advantages will greatly outweigh the disadvantages.

If you want the old way of doing things, add -DOLD_TI to your AMBERBUILD
flags. But the old code may go away sometime in the future. Also, I have
turned off the old tests for TI in amber9/test/Makefile, since they no
work. But I have not yet inserted new test cases: that should come soon.

Most people should not have to do anything, other than perhaps turning on
OLD_TI if you want to do free energy calcs in sander9 without risking
the new code.

Received on Wed Apr 05 2006 - 23:49:55 PDT
Custom Search