As a supplement to Brian's email, I don't think it's really feasible to
"fix" the density to be a value __other__ than the natural density of that
particular water model. If you enlarge the box (because you need to make
your system "less" dense), then you will get vacuum bubbles, which is
probably not what you want. If you shrink the box, as Brian said, things
will get messy. You'll have water molecules that don't even exist in the
central unit cell, but which exist elsewhere (not good!). Any attempt to
find the "minimum image distance" will almost certainly place them directly
on top of an existing water molecule, which will likely cause your system
to blow up.
I don't see any way of forcing the density to be something "unnatural" for
your particular water model short of adjusting the external pressure and
letting the barostat adjust your density -- and very large changes in
pressure are needed to effect small changes in densities. My suggestion
would be to research the available water models and choose the one that
matches the densities you wish to obtain.
HTH,
Jason
On Wed, Jan 18, 2012 at 8:45 AM, Brian Radak <radak004.umn.edu> wrote:
> John,
>
> To my knowledge, the only place that AMBER learns about system volume is in
> the coordinate file, the last line of which contains the lattice lengths
> and angles (a, b, c, alpha, beta, gamma). So long as your system already
> has the correct shape you can just re-assign the lengths manually. There
> is also a program in $AMBERHOME/bin called ChBox that will do this
> automatically, but I'm not certain of its usage/quality.
>
> If you are expanding your volume, then additional dynamics is generally
> stable in my experience. If you are contracting your volume, then things
> might get messy. I would recommend running constant pressure dynamics
> before shrinking the volume, as systems with negative virial will rapidly
> contract the simulation cell in general.
>
> Regards,
> Brian
>
> On Wed, Jan 18, 2012 at 8:28 AM, Beale, John <John.Beale.stlcop.edu>
> wrote:
>
> >
> > I need to adjust the density of my protein/explicit water system to match
> > experimental density values at a variety of temperatures. From what I
> have
> > read, to do this I should adjust the volume of the system. Can someone
> > please tell me how to do this?
> >
> > John
> >
> > John M. Beale, Jr., Ph.D.
> > Professor of Medicinal Chemistry and Pharmacognosy
> > Saint Louis College of Pharmacy
> > 4588 Parkview Place
> > Saint Louis, Missouri 63110-1088
> > Office: 314-446-8461
> > Cell: 314-315-0409
> > FAX: 314-446-8460
> > John.Beale.stlcop.edu<mailto:John.Beale.stlcop.edu>
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
> Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 18 2012 - 06:00:07 PST
