cell shape after increasing margin (parm7 ff)

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Jun 07 2012 - 01:26:35 CDT

Should it be of any interest to users of parm7 ff:

Following "Periodic cell has become too small ..." for a protein in a
tip3 water at 0.6M NaCl, increasing the margin from 5 to 10 let MD to
continue (1.5 ns), reaching constant RMSD, at const temp, press,
kinetic. Total energy had decreased until midway, then constant,
Protein RMSD OK.

However, the cell has changed from 112, 113, 97 to 113, 114, 39,
although nothing exceeds the water box, the center remained unchanged,
and the protein rmds is ok. Periodicity shown no more space between
the periodic boxes, in either direction. Why just one side only has
shrunk so much?

I plan to use the end protein in a new water box, rebuilding prmtop/inpcrd

francesco pietra

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