Hi All,
We have been working on MMPBSA calculations using the new implementation of AmberTools14 and we are getting strange results. We have used two options for decomposing the total energy into components: idecomp=2 (per residue) or idecomp=4 (pairwise).
They should not affect the total energy in the calculation.However, the total energies differ depending whether we use idecomp=2 or idecomp=4. As far as we understand the way it does the calculation is that the decomposition is after the total energies are calculated but we find differences before the decomposition.
Using GB, the results are the same for both idecomp options, but using PB the result differ.
Please, find attached an example of this calculation on exactly the same system (only changing idecomp=2 or 4).
Could you please help us on clarifying this issue?
Thanks very much!
Best,
Yoel
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Received on Mon May 26 2014 - 18:30:02 PDT
