Hello,
Is there any chance to have netCDF trajectory support for mmpbsa.py? I tried just adding netcdf to all the ptraj output, but since the final sander command gets sent to utils.py, I can't add the ioutfm=1 line in there. Sander is oh so much faster when reading binary.
General question: how are the total energies calculated for the pb method? Gb looks straightforward because everything needed to calculate the total energy is listed in the final mmpbsa.py output. As for pb... an energy term that is used to calculate the final energy is missing from the total, or mmpbsa and I disagree on how to do general floating point arithmetic.
Thank you,
Trevor Gokey
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Received on Thu Sep 16 2010 - 11:30:03 PDT
