[gmx-users] Optimization of the box size during an energy minimization?

[Tsjerk Wassenaar]

Hey :)

A little while ago I tried growing in molecules in a solution starting from
shrunken coordinates. It would have been very useful if the box also had
taken part in the energy minimization... That would have saved quite bit of
trouble relaxing with NPT MD.

Just my two cents :)

Tsjerk

On Dec 29, 2010 7:32 PM, "Justin A. Lemkul" <jalemkul at vt.edu> wrote:

MyLinkka wrote: > > Hi Justin, > > Thanks for your answer! > > As far as I
understood, the virial ...
I suppose, in theory, it's possible to use an EM algorithm to optimize a
box. But for most systems, like a box filled with solvent, during EM the
positions move very little and I'd be willing to bet the box wouldn't even
change.  I guess it depends on what you're looking to do, but for a system
that hasn't even been equilibrated under the desired thermodynamic
conditions (with a proper velocity distribution applied to the atoms), I
don't see any real value in trying to obtain what you might consider an
"optimized" box for a system that is not at equilibrium.  The box stabilizes
during NPT equilibration.

-Justin

> Ting Li > > > On 12/25/2010 3:41 PM, Justin A. Lemkul wrote: >> >> >> >>
MyLinkka wrote: >>> >>>...

======================================== Justin A. Lemkul Ph.D. Candidate
ICTAS Doctoral Scholar MI...

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