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.
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.
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
=
http://www.pas.rochester.edu/~yildirim/ =
-----------------------------------------------------------
On Wed, 3 Nov 2010, Bill Ross wrote:
>> I am trying to create a rectangular cuboid system and end up having
>> vacuum bubbles while heating the system up to 300 K.
>
> These would be expected with leap, and likely with any program
> that doesn't pack atoms carefully. The answer is to use NPT to
> equilibrate volume.
>
> Bill
>
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Received on Wed Nov 03 2010 - 15:30:04 PDT
