Re: [AMBER] How the box info is used

From: Ilyas Yildirim <>
Date: Wed, 3 Nov 2010 20:00:56 -0500 (CDT)

Tom - Thanks for the response. If I do not use any salt at all and just
use TIP3P water in between the 2 surfaces, the equilibrium trajectory does
not show any weird situation: Water molecules diffuse homogeneously in the
x and y direction. And when I look at the final structure (after using
'image' command in ptraj), I do not see any bubbles at the edges of the
unit cell. I see the bubbles forming when I use ions in the system. The
vdw parameters of the atoms on the surfaces are pretty high, but seeing a
regular behaviour in the water system implies me that it is not the
surface-water interaction causing this bubbles.

My system is similar to a membrane system, but with different conditions.
If I start with anisotropic pressure scaling (ntp=2), should I keep it
always in ntp=2? Or can I switch it back to ntp=1? I will try and see if
it will solve the bubble problem, but not seeing this problem in water
simulation makes me wonder why it does not work on 1M Na+ system.

Best regards,

   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, Thomas Cheatham III wrote:

>> 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).
> --tec3
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Nov 03 2010 - 18:30:02 PDT
Custom Search