From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Feb 10 2010 - 11:52:30 CST
On 10 February 2010 15:16, Rick Calloway <rick_at_cnainc.net> wrote:
> Hi community,
> Can someone help me understand the relationship between the 3 by 3 pressure
> tensor ouptut on the PRESSURE: line and the single number printed under the
> PRESSURE column heading on the ENERGY: line?
> I assume they are both in bar so is there a tensor matrix operation that is
> done on the 3x3 matrix that results in a single magnitude?
The scalar pressure is one-third the trace of the stress tensor (which
really means the average of the diagonal elements).
> Second, when profile pressures are output the result is only a single 3
> column vector. When looking for the instantaneous pressure along the
> profile (like in Justin Gullingsrud's paper on Lipid Bilayer pressure
> profiles) what does the 3 col vector represent
That's in the user's guide, see the pressureProfile keyword.
> and how are the normal and
> lateral pressures calculated?
Should be clear when you have the answer to the previous question.
> Lastly, the documentation between 2.6, 2.7b1 and 2.7b2 is a little
> confusing as to what is included in the runtime output. When doing PME is
> the profile pressure output complete or does the PME contribution to
> pressure still have to be calculated from the dcd file later and added in?
Yes, the two-step process is the only way, unfortunately. Only
post-processing the trajectory will give you the long-range PME
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