On Mon, Oct 29, 2012, Mo Chen wrote:
>
> It seems the Molecular Virial is the 3d stress/pressure tensor matrix.
I think this is wrong. The pressure is determined by a combination of the
virial and kinetic energy terms. See code around line 911 of runmd.F90.
Athough sander computes the full virial tensor (I think for conversion back
from non-orthogonal unit cells), it only computes the diagonal components of
the pressure tensor. I think extra coding would be required to get more.
> However, my system is a cubic box, and the output shows that the
> stress/pressure tensor matrix is not symmetric. I found in Amber Manual
> that when ncsm is applied to a periodic system, it only remove the
> translational COM motion, but not the rotational COM motion.
This is correct. There is no way to remove rotational motion in an infinite
periodic system, (and not way for such components to build up in the first
place.) If you are concerned about this, you can set nscm to zero to turn
this off.
cc-ing to Dave Cerutti, who has looked into this stuff more than I have.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 29 2012 - 07:30:06 PDT
