Dear Amber Users,
When running an MD is the water “buffer zone” maintained on all sides of your protein? For example, if you have a period box with dimensions 63x55x78 angstroms and the van der waals radius of your protein is 44x35x59 angstroms would you ever encounter a situation where the protein rotated and now the long edge of your protein is aligned with the short edge of the box and you would have a potential interaction with the periodic image. I have not seen this happen but the question has been posed. Any insight would be appreciated.
Janet Paulsen
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Received on Fri May 30 2014 - 09:00:02 PDT
