[AMBER] periodic box size

From: Rui Chen <rchen6.ualberta.ca>
Date: Thu, 29 Aug 2019 18:58:54 -0600


I am running MD simulation with NAMD, I prepare the protein (solvation,
ionization, making S-S bonds, connect glycans and ASN) using tleap. I'd
like to get the periodic box size. In leap.log file, is the total vdw box
size the correct answer? (e.g.: Total vdw box size:
84.291 81.320 135.912 angstroms.) Where can I get the information of the
box centre? Since the box generated by leap includes a buffer, it's size is
bigger than the true box size, should I get the box size from tleap or use
VMD script? Thank you.

Best regards,
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Received on Thu Aug 29 2019 - 18:00:01 PDT
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