Re: [AMBER] How the box info is used

From: Ilyas Yildirim <>
Date: Wed, 3 Nov 2010 17:22:24 -0500 (CDT)

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

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 =
   = =

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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Nov 03 2010 - 15:30:04 PDT
Custom Search