Re: [AMBER] protein in popc bilayer simulation

From: David A Case <>
Date: Thu, 26 Sep 2013 07:46:01 -0400

On Thu, Sep 26, 2013, Wang Chern Hoe (Dr) wrote:
> My experience indicated that taup had a drastic effect for NPT and NPgT
> simulations which run into skinnb errors,

Using a large taup slows down the rate at which the box changes size, which
may appear to help the code respond to such changes. But it also really
reduces the fluctuations in volume once you have reached the equilibrated
box size. So, it may make sense to use increase taup during equilibration,
when you are far from from the correct box size and density, but it seems
dangerous to use values greater than 1 ps or so for a "production" phase of
the simulation. (Even a 1ps, volume fluctuations are smaller than they should
be for a canonical ensemble; we are working on better barostats.)

Caveat: I've not done lipid simulations. As Ross says, there may be some
other source of your particular problems.


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Received on Thu Sep 26 2013 - 05:00:03 PDT
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