On Wed, Aug 24, 2022, Matthew Guberman-Pfeffer via AMBER wrote:
>
>I’m wondering if the idecomp output is available in PMEMD for thermodynamic
>integration calculations. The manual makes it clear that it’s available in
>SANDER, but I wanted to check if it’s also available in PMEMD. If not, is
>there another way to get a per-residue decomposition of dv/dl?
You can see in Section 21.2 of the Reference Manual ("Functionality" in
pmemd) that idecomp!=0 is not supported in pmemd. And, don't be afraid to
experiment: you'll get the same message if you try to run pmemd with idecomp
> 0.
Bear this in mind: Although the free energy change (obtained by integrating
the average of dv/dl) is independent of path that lambda takes in going from
0 to 1, the individual pieces of it are not. So a decomposition is not
well-defined. It may have some qualitative or heuristic use, however.
....dac
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Received on Thu Aug 25 2022 - 06:30:03 PDT
