RE: [AMBER] How to make ionic liquid solvent box?

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 4 May 2010 15:44:14 -0700

The email format is encoded to a point that is hard for me to
decrypt with my primitive email setup, but I note:

> Added 2 residues.

You will probably need to make the box cutoff much bigger to
get more residues in there. Presumably the box will shrink a
lot on equilibration (constant pressure). However for test
puroposes having a few residues might be useful, so I would
run some tests with what you have to see if things blow up.

> my ion structures have been changed.

If you mean the coordinates have been changed, e.g. by shifting
them into a box, that is normal.

Bill

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Received on Tue May 04 2010 - 16:00:04 PDT
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