Re: [AMBER] why are pres_X, pres_Y, and pres_Z different?

From: case <>
Date: Fri, 25 Oct 2013 18:23:17 -0400

On Fri, Oct 25, 2013, Jose Borreguero wrote:
> I am trying to equilibrate a system in the NPT ensemble. I set the
> following pressure settings:
> ntp=1, !isotropic position scaling
> pres0=1.013, !reference pressure
> taup=2.0, !relaxation time (psec)
> comp=44.6, !compressibility
> My system is not cubic, but hexagonal:
> Lx Ly Lz alpha beta
> gamma:
> 36.43534 36.43534 3.17648 90.00000 90.00000 120.00000

Oooh...what kind of system is this, with such a large discrpancy in unit cell
lengths? I'm kind of surprised that Amber (is this sander or pmemd?) would
even run with a cell length of only 3.2 Ang. What does it say in the output
about the "Largest sphere to fit in the unit cell"?

> After the run, the pressures taken from file mdend average to:
> <pressure>: 15.0
> <press_x>: 259.9
> <press_y>: 301.2
> <press_z>: -515.5 !!!!!

This looks about right to me: the volume scaling is only making the total
pressure close to the target, and doesn't care about the individual terms.
Without know what sort of system this is, it's hard to say how long it might
take (if ever) to equilibrate to a system with equal pressures.


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Received on Fri Oct 25 2013 - 15:30:02 PDT
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