"GroupPressure no" resulting in negative pressure outputs

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

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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.

Thanks,
Sebastian

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