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

From: Bill Ross <>
Date: Wed, 9 Dec 2009 09:46:59 -0800 (PST)

> 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.


AMBER mailing list
Received on Wed Dec 09 2009 - 10:00:02 PST
Custom Search