Re: Pressure Discrepancy

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Wed Mar 28 2007 - 12:40:23 CDT

*There is one suggestion, which is to use NVT ensemble, by having
different box sizes and choose the box size that gives you the right
pressure. This suggestion is fine if you can use NVT ensemble, which
varies the pressure and keeps the box size constant.

Unfortunately, this suggestion is not suitable for my case, since I have
to use NPAT ensemble.

I think there are some bugs in the NAMD algorithms, since I found other
two problems. I was not able to constrain the com of my protein around
the origin for whatever the force constant I use in both SMD or Free
Energy of Conformational Change Calculations.

I sent a copy of my notes to James Phillips, NAMD developer, hopping to
here back from him soon.

Thanks

Morad Alawneh
**
*
tamal_at_iitk.ac.in wrote:
> I am also finding the same problem.It never relates with our input
> pressure.Have you got any reply?.
> Thanks for your referred paper in your mail.It is really a fundamental paper.
>
> thanks
> Tamal Banerjee
>
>
>> *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
>>
>>
>> **
>>
>>
>>
>> *
>>
>>
>>
>
>
> *****************************************
> Tamal Banerjee
> Research Scholar
> Department of Chemical Engineering
> I.I.T Kanpur
> Phone: +91-512-2597533 (Lab)
> +91-512-2595433 (Residence)
> URL: home.iitk.ac.in/~tamal
> *****************************************
>
>

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