Drs. Ross, Owczarzy and Walker,
Thanks for your well-informed answers -- it appears that one
wants to have a water buffer that is large enough to not be
affected by box size changes or molecular rotation during
simulation which might invalidate long-range force calculations
(or cause calculation costs to go hyperbolic)!
Best Regards,
Bob Hopkins
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
Behalf Of Ross Walker
Sent: Friday, December 11, 2009 9:47 PM
To: 'AMBER Mailing List'
Subject: [Possible Spam: 10%] RE: FW: Solvent/solute ratio? Re: [AMBER]
how to add desirednumberof water
Hi Robert,
Be aware that it is also a function of simulation length. You need to
make
sure your molecule is solvated by enough solvent throughout the
simulation.
In the tutorial the timescales are fairly short so the DNA does not
rotate
or change shape / size very much. If you run a longer simulation where
it
can rotate, or might fold up / unfold then you would need a larger water
box, or for DNA ideally a truncated octahedron to allow for rotation.
Thus I
would suggest a minimum of 8 angstroms buffer but ideally more if you
think
there will be changes in the box size, protein shape etc.
In the best case it should probably be as much as you can afford.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Bill Ross
> Sent: Friday, December 11, 2009 2:20 PM
> To: amber.ambermd.org
> Subject: Re: FW: Solvent/solute ratio? Re: [AMBER] how to add desired
> number of water
>
> > How *does* one estimate an appropriate amount
> > of solvent for a given solute molecule in a MD simulation in
> explicit=20
> > solvent?
>
> My sense of it is, you want more than your cutoff, by some margin
> to allow for box shrinkage during equilibration. For nucleic acids,
> I have used 10A water (before adding ions) with 8A cutoff.
>
> Bill
>
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Received on Sat Dec 12 2009 - 17:00:02 PST
