Re: [AMBER] NVE ensemble for solvation

From: David A Case <>
Date: Wed, 10 Oct 2012 07:08:50 -0400

On Tue, Oct 09, 2012, marawan hussain wrote:

> I have a silly question regarding solvation shells for
> nucleosides...Is it a better option to run the production simulation in
> the NVE ensemble rather than either NPT or NVT ensembles..?...I feel
> like with either NVT or NPT we are imposing some artificial constraints
> on the water molecules...Does any body made a careful comparison to test
> the best option for such purpose....???

It's not very clear what you mean by "such purpose". If you interested
in equilibrium (time independent) behavior in the canonical ensemble,
then NPT is probably a better choice. If you are interested in dynamical
(time-dependent) behavior (such as water residence times, for example)
then you should use NVE. [If you want both, use NVE, since the difference in
equilibrium behavior is generally quite small, especially as you move towards
having lots of waters.]


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Received on Wed Oct 10 2012 - 04:30:03 PDT
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