AMBER Archive (2009)

Subject: FW: Solvent/solute ratio? Re: [AMBER] how to add desired number of water

From: Hopkins, Robert (hopkins_at_uhcl.edu)
Date: Fri Dec 11 2009 - 16:05:51 CST

Dear Amber Users and Developers,

The e-mail below from Bill Ross brings up an important question and also
raises a serious concern. How *does* one estimate an appropriate amount
of solvent for a given solute molecule in a MD simulation in explicit
solvent? The thought of wasting hundreds (or thousands) of wallclock
hours doing a simulation that is subsequently rejected by a journal
reviewer as having too little solvent is seriously disturbing.

In the basic Amber Tutorial B1 by Ross Walker, it appears that an 8
Angstrom
thick blanket of TIP3P water is adequate for a duplex poly(dA)-poly(dT)
DNA
decamer. I am working with a duplex DNA dodecamer and have, likewise,
used
an 8A layer of TIP3P solvent in a truncated octahedral box. There are
758
atoms in the DNA and 4120 explicit waters (12,360 solvent atoms) as
solvent.
What are some criteria for knowing if this is an adequate solvent/solute

ratio (especially from a reviewer's standpoint)?

I would greatly appreciate any comments or suggestions. Thanks,

Bob Hopkins, Professor Emeritus
Chemistry and Physics
University of Houston - Clear Lake

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
Behalf Of Bill Ross
Sent: Wednesday, December 09, 2009 11:47 AM
To: amber_at_ambermd.org
Subject: Re: [AMBER] how to add desired number of water

> 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

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber