From: Sterling Paramore (paramore_at_hec.utah.edu)
Date: Wed Mar 28 2007 - 15:43:55 CDT
What is the standard deviation of the pressure you measured and how long
were your simulations?
-Sterling
Morad Alawneh wrote:
> *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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