MyLinkka wrote:
Hi Justin,
Thanks for your answer!
As far as I understood, the virial expression of pressure has two parts,
the kinetic energy contribution and the potential energy contribution.
Even when
temperature is undefined or zero, the product of pair force and distance
between
atoms still contribute to the microscopic pressure tensor. In the EM
algorithm,
if this pressure tensor is included in the target function to be
minimized, it should
be able to optimize the box size as well as the atom positions, because
the pressure
tensor is a functional of box size.
However, it's good to know that Gromacs is not doing this task. Thanks!
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:
Yeah! Energy minimization with pressure coupling.
Is this possible?
No. There are no velocities in EM, and hence no kinetic energy, no
virial, and thus no pressure coupling.
-Justin
Ting
On 12/24/2010 5:04 AM, Terry wrote:
On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 24/12/2010 5:17 AM, MyLinkka wrote:
Does anybody know if it is possible to optimize the box
size during an energy minimization in Gromacs?
Optimize for what criterion?
Can I make pressure coupling if it's possible?
Do you mean energy minimization with pressure coupling?
Terry
Sure, that's in the manual and covered in tutorials.
Mark
Is there a workaround if there is no direct way?
Thanks!
Ting
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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