Re: fixed atoms / pressure

From: Peter Freddolino (
Date: Wed Mar 12 2008 - 18:55:07 CDT

Hi Arturas,
what units are you using for water density here? Also, is the PRESSURE
value you're reporting averaged over the entire run? Are you sure you
ran long enough for it to be equilibrated?

Using constant pressure with a lot of fixed atoms (eg, the whole quartz
slab) is probably not a good idea in general... if you must, you might
want to try with fixedAtomForces on, but you're probably better off
applying constraints to a few atoms.

Also, how large is your water layer above and below the quartz slab? And
how are you calculating the density of water in your (heterogeneous)


Arturas Ziemys wrote:
> Hi,
> I need some insights and comments.
> MY SYSTEM: quartz slab (~15 A wide; patched to mimic infinite layer)
> on XY plane and TIP3P water on both sides of Z. useFexibleCell is ON.
> useConstantArea is ON.
> PROBLEMS: 1) I get higher water density (~0.037) than TIP3P "standart"
> (~0.033-0.034) at NPT/1bar. 2) PRESSURE fluctuates around very low
> values (~ -1000 bars).
> However, my quartz is minimized and fixed after. I get higher water
> density using system with with fixed and not fixed quartz slab.
> QUESTIONS: How necessary to use useFexibleCell ON and useConstantArea
> ON in my case ?
> Best
> Arturas

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:47:37 CST