[gmx-users] Can we calculate Potential of mean force from normal MD simulations

[André Farias de Moura]

yes and no.

from the standpoint of statistical mechanics, there is nothing wrong at all
with this approach, but convergence is certainly an issue, since
equilibrium MD will sample efficiently only low-lying states.

maybe you might want to take a look at chapter 7 of Berendsen's textbook
"SIMULATING THE PHYSICAL WORLD Hierarchical Modeling from Quantum Mechanics
to Fluid Dynamics"

Andre


On Wed, Jun 14, 2017 at 11:10 AM, Apramita Chand <apramita.chand at gmail.com>
wrote:

> Dear All,
> Suppose we have executed a normal MD simulation without using umbrella
> sampling or pull techniques. If we have the g(r), can we plot potential of
> mean force between some solutes using this equation?
>
>
> yours sincerely,
> Apramita
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090