Fwd: About "add solvation"

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jan 21 2013 - 03:49:06 CST

Sorry I forgot VMD (I used the last version for Linux)

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Mon, Jan 21, 2013 at 10:42 AM
Subject: namd-l: About "add solvation"
To: NAMD <namd-l_at_ks.uiuc.edu>

I am observing a curious behavior in adding the solvation box, and
subsequent addions, with a heme protein. That is, to the dispdev
generated psf/pdb, add solvation (TIP3) produces a much elongated box
(X=102, y=63, z=75), from one side where there is nothing special
about this nearly spherical protein. Subsequent add ions (Na+, to
neutrality) places some Na+ in the elongated area, far away from the

As I said, all files in /parts, used for dispdev, are clean, free from
anything that would require solvation (and neutralization).

I understand that without seeing it is difficult to grasp what is
peculiar there. Perhaps similar affairs have already been noticed.


francesco pietra

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