Thank you for the explanation.
On Mon, Jun 2, 2014 at 5:05 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, 2014-06-02 at 16:23 +0530, Saikat Dutta chowdhury wrote:
> > Hi Amber Users,
>
> > So my question "As I am running NPT simulation, should I be worried that
> > PRESS is not remaining constant or is the fluctuation is natural in
> AMBER?"
>
> This is completely normal. It helps to understand how molecular
> dynamics simulations maintain a "constant pressure". The underlying
> idea is that the volume is scaled to keep the pressure, on average,
> constant. As we know from our first chemistry course, solids and
> liquids are largely incompressible, meaning that they have a very small
> isothermal compressibility (which is 1/V * dV/dp where V is volume and p
> is pressure). If this ratio is small, it is clear that even small
> changes in volume can yield large changes in pressure.
>
> While the pressure fluctuates a lot in an MD simulation, the volume does
> not. Therefore, the best way to monitor the stabilization of the unit
> cell volume is to monitor the density, not the pressure.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
--
Saikat Dutta Chowdhury
Email: pbr322.dutta.gmail.com
Mob:
8017650842
9681144106
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Received on Mon Jun 02 2014 - 05:00:03 PDT
