From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Wed Mar 28 2007 - 13:16:47 CDT
Are you using multiple time stepping?
On Wed, 28 Mar 2007, Morad Alawneh wrote:
> *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.
> 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.
>> 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
>>> 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
>>> 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>?
>>> 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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