Re: [AMBER] How the box info is used

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Wed, 3 Nov 2010 15:34:27 -0700

> 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
> pretty reasonable after the equilibration. When the system has 1 M of salt
> in it, however, water molecules are sucked such that it creates vacuum
> bubbles. And they get bigger even after continuing the simulation with
> NPT.

It might be useful to see all your equilibrateion mdin files. I'd
say the NPT should be run until density reaches 1, then switch to
NVT and the bubbles can't form :-) It might be convenient to do
this at lower temperature, though this problem might be worth
understanding better before moving on.

What salt are you using? Do the vacuum bubbles form at the ions?
How many waters, how many ions?

> I was going to send a second email regarding vacuum bubble problem I am
> having in my system, but one of my collegue said that it might be a
> problem with the box information. As a result, I wanted to understand how
> sander and pmemd use the boxinfo in periodicity and calculations.

Did you solvate with leap? No matter what the box is, NPT should fix
any vacuum.


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