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
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
On Thu, 23 Dec 2010 19:17:04 +0100
MyLinkka mylin...@gmail.com wrote:
Does anybody know if it is possible to optimize the box size
during an energy minimization in Gromacs?
Can I make pressure coupling if it's possible?
Is there a workaround if there is no direct way?
On a related
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
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
Yeah! Energy minimization with pressure coupling.
Is this possible?
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
Hi Mark,
Forgive me asking a question that may be obvious for experienced GMX users.
I want to quickly verify a problem against some other software, so I
temporarily turn to Gromacs.
It would be nice if you could point me out where to find the relevant tutorial
or manual chapter.
I couldn't
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
Does anybody know if it is possible to optimize the box size during an
energy minimization in Gromacs?
Can I make pressure coupling if it's possible?
Is there a workaround if there is no direct way?
Thanks!
Ting
--
gmx-users mailing listgmx-users@gromacs.org
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?
Sure, that's in the manual and covered in tutorials.
On Fri, Dec 24, 2010 at 5:36 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
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
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