[gmx-users] Pressure of an energy minimized system

[Rakesh Sharan]

Thanks very much Mark! A good use of this quantity (pressure of energy
minimized structures) is to understand the thermodynamic behavior of
"inherent structures" (energy minimized structures). These inherent
structures provide valuable information about the underlying potential
energy landscape of a system and are becoming increasing popular in both
biological (e. g. see http://www.pnas.org/content/103/14/5279.full ) and
materials (e.g. see
http://www.nature.com/nature/journal/v393/n6685/full/393554a0.html)
sciences. I would highly recommend to keep this feature and make sure that
it correctly computes the virial pressure.

Best,
Rakesh

----------------------------------------------------
Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544


On Tue, Mar 8, 2016 at 9:41 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> We discussed this recently at
>
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2015-October/008710.html
> .
> Whether it correctly computes the well defined quantity isn't known;
> neither does anybody know of a good use for it!
>
> Mark
>
> On Tue, 8 Mar 2016 14:31 Rakesh Sharan <rs11chembhu at gmail.com> wrote:
>
> > Dear all,
> >
> > I have a question regarding computation of pressure of an energy
> minimized
> > (using steepest decent) system. I would expect that the pressure of an
> > energy minimized system should have contribution only from the virial
> part
> > of the pressure expression (as there is no temperature). However, when I
> am
> > computing pressure using g_energy, the pressure (P_tot) and pressure
> > computed from virial (P_vir = (-1/3Vol)*(Vir_xx+Vir_yy+Vir_z)/3)) are
> > significantly different and P_tot is exactly six times P_vir. I am not
> able
> > to understand the origin of this discrepancy. I would highly appreciate
> > comments/suggestions from this forum. I would also very much appreciate
> any
> > alternate suggestion for computing pressure of energy minimized
> structures.
> >
> > Thanks very much!
> >
> > Best,
> > Rakesh
> >
> > ----------------------------------------------------
> > Rakesh S. Singh, Ph.D.
> > Postdoctoral Research Associate,
> > Department of Chemical & Biological Engineering,
> > Princeton University,
> > Princeton, NJ 08544
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