AMBER: thermodynamic integration

From: Cooper, Matthew <>
Date: Thu, 8 Nov 2007 16:14:25 -0500


I am experiencing difficulties with thermodynamic integration in Amber

I use the same input deck for numerous integrations. Occasionally, there
will be no data for DV/DL, though a summary will be printed that
contains only zeros.

Rerunning the script will sometimes result in DV/DL averages being
calculated though not always. If I run two molecules with identical
starting positions but different charges, one may fail while the other
will not.

Does anyone have any experience with this?

David wrote a while ago, in response to a similar question:

<<Are you sure that the two Hamiltonians are really different? Try a
run with clambda=0, and with clambda=1 to make sure you are really
different energies. (The behavior you report, not geting DV/DL at each
step, but still getting a summary, with all values zero, is consistent
with not having any energy difference between the two Hamiltonians.)>>

I have checked - the energies are different at clambda = 0 and clambda =
1, at least according to the average after 1250 steps.



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Received on Sun Nov 11 2007 - 06:07:33 PST
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