"GroupPressure no" resulting in negative pressure outputs

From: Sebastian Stolzenberg (s.stolzenberg_at_gmail.com)
Date: Thu Nov 25 2010 - 13:51:13 CST

Happy Thanksgiving, All,

"useGroupPressure no" is a default option and not required, when not
using "rigidBonds".

For the following, I measure "pressure" from the log files using the
NAMD Plot plugin by observing "PRESSAVG" or "GPRESSAVG".

For a system with box size >100x100x90A^3 and no rigidBonds
(FlexibleCell yes):
Using "useGroupPressure yes",
I get pressures of about 1+-2bar
and with "useGroupPressure no",
I get pressures of about -13+-3bar

Fluctuations are larger for "useGroupPressure no" vs. ""useGroupPressure
yes", but within these fluctuations, the "useGroupPressure no" doesn't
seem to give me the correct pressure that I set via:

LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 50
LangevinPistonTemp 310
PME yes
PMEGridSpacing 1.0

Talking to colleagues of mine, they appear to have exactly the same
issue for different systems.

I am happy to share log files and input scripts, if needed.


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