AMBER Archive (2009)

Subject: Re: [AMBER] how to add desired number of water

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Dec 09 2009 - 11:46:59 CST

> slovatebox model TIP3PBOX 8.0
> it adds 2800 water residues=2C suppose i need to add only 2000 residues of =
> water molecule

First, 8.0 is small for a box. 10 would be more reasonable.

In any case, you could try different cutoffs (7.9 to start) and
try to get close to the number you want. You can also edit the
system in xleap and delete waters.

But because of small box, your simulation may be suspect, e.g. to
reviewers if you plan to publish.

Bill

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