Re: [AMBER] How the box info is used

From: Thomas Cheatham III <>
Date: Wed, 3 Nov 2010 16:30:48 -0600 (Mountain Daylight Time)

> Yes, the threads in the mailing list always says that NPT has to be used
> in order to get rid of vacuum bubbles. I do use NPT in the equilibration
> process. The problem is dominant when I have a salt concentration around 1
> M. In a test system, when I do not have any salt at all, the system looks

It if it is NPT and bubbles are forming, there must be some force opposing
the pressure (perhaps slab - slab repulsion) that is strong enough to
overcome the water-water attraction. You could try to crank up
the pressure coupling constant.

Alternatively, you could try anisotropic pressure coupling or only
coupling in specific directions (we did this with our salt crystal : water
simulations although the latter requires some code modifications). I
think that both coupling in a single direction and anisotropic coupling
worked for us. Note that we did not observe such bubble problems in a
full 2D slab (salt crystal) w/ water (Joung/Cheatham, 2009, JPCB 113,
13279) and we were at saturated salt concentrations (i.e. above 1 M).


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Received on Wed Nov 03 2010 - 16:00:02 PDT
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