Re: [AMBER] protein in popc bilayer simulation

From: David A Case <>
Date: Fri, 27 Sep 2013 07:39:12 -0400

On Fri, Sep 27, 2013, Wang Chern Hoe (Dr) wrote:
> I use taup=20 for a ~ 2-3 ns duration NPT equilibration...
> For the equilibration phase...
> The density continued to increase over 10 ns, so more time is required
> for a full equilibration.

I don't have a particular problem with using such schemes for equilibration.
As I said, I don't have experience with bilayer simulations, and don't know
what you really mean by "rather dramatic change in the box dimensions".

But *at equilibrium*, large values of taup will suppress volume fluctuations,
effectively making the results much more like those from a constant volume
simulation than they should be. It is not possible to know in general how
important the differences between ensembles will be in a given situation.


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Received on Fri Sep 27 2013 - 05:00:03 PDT
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