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

From: Jose Borreguero <borreguero.gmail.com>
Date: Fri, 25 Oct 2013 11:42:02 -0400

Dear AMBER users,

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
36.43534 36.43534 3.17648 90.00000 90.00000 120.00000

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 !!!!!

I wanted to have a system where the pressure is the same no matter which
axis, as you would have for a cubic system. Is this an artifact of the

Note: EKCOM_X, EKCOM_Y, and EKCOM_Z are all the same. However, Virial_Z is
much higher than Virial_X and Virial_Y.

Any info is much appreciated.
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Received on Fri Oct 25 2013 - 09:00:05 PDT
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