Dear amber developers,
We are currently using MMPBSA.py.MPI to compare the results with Delphi.
The following is the setting we use:
Input file for running PB
&general
keep_files=2,
/
&pb
istrng=0.150, fillratio = 2.0,
/
Here are two questions:
1. In Amber PBSA, we are allowed to set IPB to 1 to make sure pbsa is using
the exactly same surface defination as Delphi. Since we are not aware any
adjustable IPB related setting in MMPBSA.py.MPI, may we know if we are able
to set IPB related setting in MMPBSA.py.MPI? Or the default setting of IPB
is 1 in MMPBSA.py?
2. Also, Delphi sets the boundary condition by bndcon=4 and Amber “pbsa”
sets the boundary condition as BCOPT = 5. So are the boundary condition
setting in MMPBSA.py.MPI the same as in Delphi?
Best,
Henry
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Received on Sat Dec 08 2012 - 11:30:02 PST
