Pressure Discrepancy

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Tue Mar 27 2007 - 13:23:42 CDT

*Dear NAMD Developers and users,

I am trying to evaluate the surface tension of my system (a protein
surrounded by a lipid bilayer in water and salt) using this equation:
0.5*Lz*(Pzz - Pt), where

Lz: the box length in z direction, which is the reaction coordinate.
Pzz: the pressure sensor in z direction
pt = 0.5*(Pxx + Pyy)

I am using the NPAT ensemble with the following settings in NAMD2.6:

# Langevin Dynamics Parameters
langevin on
langevinTemp 303.15
langevinDamping 5.0
langevinHydrogen on
# Pressure Control
useGroupPressure yes
useFlexibleCell yes
useConstantRatio no
useConstantArea yes
# Nose-Hoover Langevin Piston Pressure Control
LangevinPiston on
LangevinPistonTarget 1.01325 ;# 1 atm 1.01325 bar
LangevinPistonPeriod 200.0
LangevinPistonDecay 500.0
LangevinPistonTemp 303.15
# Periodic Boundary Conditions
cellBasisVector1 40.0 00.0 00.0
cellBasisVector2 00.0 40.0 00.0
cellBasisVector3 00.0 00.0 90.0
cellOrigin 0.0 0.0 0.0
wrapWater on
wrapAll on
wrapNearest off

According to the article
** ZHANG YH, FELLER SE, BROOKS BR, et al.
COMPUTER-SIMULATION OF LIQUID/LIQUID INTERFACES .1. THEORY AND
APPLICATION TO OCTANE/WATER
<http://apps.isiknowledge.com/WoS/CIW.cgi?SID=2EPNc3mJfLCGDA6hnmm&Func=Abstract&doc=9/5>
JOURNAL OF CHEMICAL PHYSICS 103 (23): 10252-10266 DEC 15 1995 *
*Pzz should take the value of Pn, which is ~ 1 bar, but when I tested
its values it had different values.
If I take the average of those pressure values, they are far away from 1
bar, here is an example:

Pxx Pyy Pzz Pt
P <P>
720.2230 415.1900 -427.7030 567.7070 235.9037 235.9037
196.3230 577.8960 266.0390 387.1090 346.7525 107.5640
............... ............... ...............
................ ............... .............
**simulation average: -16.4359 -112.3742 -80.3948 -54.0773

I know there is a huge fluctuations in pressure, but the average values
should take care of that and be close to 1 bar for Pzz, P, or <P>.
 
Would you explain to me why do I have this kind of pressure discrepancy
for Pzz, P, or <P>?

Thanks

Morad Alawneh

**

*

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