Re: How to confirm water box is big enough?

From: Jin Liu (jliunih_at_gmail.com)
Date: Tue Mar 30 2010 - 17:09:06 CDT

Hi Giacomo,

Many thanks for the help. Is it possible that you could explain a little
more about "the average
projection of the water molecules' dipole moments on the distance vector
from the protein"? Why is this the best checks? When this number goes to
zero, it means no electrostatics interaction between images? And how to
check this number? Thanks.

Jin

On Tue, Mar 30, 2010 at 5:38 PM, Giacomo Fiorin
<giacomo.fiorin_at_temple.edu>wrote:

> Hi Jin, ideally, you'll want that two periodic images of the protein
> are always farther than twice the van der Waals cutoff: this way they
> would not only be out of range for their mutual interaction, but also
> that they don't interact with the same water molecules.
>
> If you used 10 as cutoff, you should be almost fine (give or take 1
> water molecule). FYI, it is becoming much more commonplace to use a
> larger cutoff (e.g. 12 ).
>
> One thing you can do to make sure, is to compute the average
> projection of the water molecules' dipole moments on the distance
> vector from the protein. If the number goes to zero before the 10
> maximum distance, in my opinion it's one of the best checks that you
> can provide.
>
> Giacomo
>
> ---- ----
> Giacomo Fiorin
> ICMS - Institute for Computational Molecular Science
> Temple University
> 1900 N 12 th Street, Philadelphia, PA 19122
> work phone: (+1)-215-204-4216
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_at_gmail.com
> ---- ----
>
>
>
> On Tue, Mar 30, 2010 at 3:29 PM, Jin Liu <jliunih_at_gmail.com> wrote:
> > Hi,
> >
> > I did a few MD simulations with the the minimum distance from the protein
> to
> > the edge of the water box as 10 angstrom. The simulations ran smoothly
> > without any problem. I am wondering what I could do to confirm the water
> box
> > is big enough? Should I measure the distance between the protein and its
> > image in the other boxes during the simulation? Or what else can I do to
> > convince people that the water box is not too small?
> > Thank you very much.
> > Best regards,
> > Jin
> >
> >
>

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