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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Received on Mon Jun 02 2014 - 05:00:03 PDT
