Agree! For most of the simulation of biological systems, EM with pressure
coupling is
not really necessary. However, it's maybe useful in some studies,such as the
simulation of
a peptide crystal. Anyway, thanks for the answer! Happy new year!
Ting
On 12/29/2010 7:31 PM, Justin A. Lemkul wrote:
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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