[gmx-developers] jarzynski/slow growth

[David Mobley]

All,

So I am getting ready to run some calculations where I restrain a
protein to a reference structure, and then gradually release the
restraints in a time-dependent way using the free energy code and
GROMACS' facility to have different restraints for the A and B states.

I need to be able to get out the work done in releasing the
restraints, at every step (for Jarzynski, in case anyone is curious).
Can anyone think of an easy way to do this?

Also, the catch is that I need to be able to do it without writing the
potential energy to an .ene file every step, because of bandwidth
restrictions on the size of the .ene files (need them to be smaller
than a few MB). Here are a couple ideas I had:

(1) Modify the code to take the difference in potential energy from
each step to the next, which will be W; keep a running total of the
integrated W, and write this out to the .ene file every time the .ene
file is dumped, as with the rest of the energies.
(2) If dH/dlambda is correct for time-dependent position restraints,
then dH/dlambda is probably the work value I'm interested in. Do the
current dH/dlambda averages printed out in the log file include *all*
of the steps? If not, is the integrated dH/dlambda tracked anywhere in
a way that includes all of the steps?

If (1) turns out to be the best option, would the developers be
interested in including this in CVS, etc., after I get it working, so
that it will persist in future versions?

Thanks,
David Mobley
UCSF