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Agree! For most of the simulation of biological systems, EM with
pressure coupling is<br>
not really necessary. However, it's maybe useful in some
studies,such as the simulation of<br>
a peptide crystal. Anyway, thanks for the answer! Happy new year!<br>
<br>
Ting<br>
<br>
On 12/29/2010 7:31 PM, Justin A. Lemkul wrote:
<blockquote cite="mid:4D1B7E98.9090308@vt.edu" type="cite">
<br>
<br>
MyLinkka wrote:
<br>
<blockquote type="cite">Hi Justin,
<br>
<br>
Thanks for your answer!
<br>
<br>
As far as I understood, the virial expression of pressure has
two parts,
<br>
the kinetic energy contribution and the potential energy
contribution. Even when
<br>
temperature is undefined or zero, the product of pair force and
distance between
<br>
atoms still contribute to the microscopic pressure tensor. In
the EM algorithm,
<br>
if this pressure tensor is included in the target function to be
minimized, it should
<br>
be able to optimize the box size as well as the atom positions,
because the pressure
<br>
tensor is a functional of box size.
<br>
<br>
However, it's good to know that Gromacs is not doing this task.
Thanks!
<br>
<br>
</blockquote>
<br>
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.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Ting Li
<br>
<br>
<br>
On 12/25/2010 3:41 PM, Justin A. Lemkul wrote:
<br>
<blockquote type="cite">
<br>
<br>
MyLinkka wrote:
<br>
<blockquote type="cite"> Yeah! Energy minimization with
pressure coupling.
<br>
Is this possible?
<br>
<br>
</blockquote>
<br>
No. There are no velocities in EM, and hence no kinetic
energy, no virial, and thus no pressure coupling.
<br>
<br>
-Justin
<br>
<br>
<blockquote type="cite">Ting
<br>
<br>
<br>
On 12/24/2010 5:04 AM, Terry wrote:
<br>
<blockquote type="cite">
<br>
<br>
On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham
<<a class="moz-txt-link-abbreviated" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>
<a class="moz-txt-link-rfc2396E" href="mailto:Mark.Abraham@anu.edu.au"><mailto:Mark.Abraham@anu.edu.au></a>> wrote:
<br>
<br>
On 24/12/2010 5:17 AM, MyLinkka wrote:
<br>
<blockquote type="cite">
<br>
<br>
Does anybody know if it is possible to
optimize the box
<br>
size during an energy minimization in Gromacs?
<br>
<br>
</blockquote>
<br>
Optimize for what criterion?
<br>
<br>
<br>
<blockquote type="cite"> Can I make pressure coupling
if it's possible?
<br>
</blockquote>
<br>
<br>
Do you mean energy minimization with pressure coupling?
<br>
<br>
Terry
<br>
<br>
<br>
Sure, that's in the manual and covered in tutorials.
<br>
<br>
Mark
<br>
<br>
<br>
<blockquote type="cite"> Is there a workaround if there
is no direct way?
<br>
<br>
Thanks!
<br>
<br>
Ting
<br>
</blockquote>
<br>
<br>
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<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
</blockquote>
<br>
<br>
</blockquote>
<br>
</blockquote>
<br>
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