Re: outputPressure

From: Morad Alawneh (alawneh_at_chem.byu.edu)
Date: Mon Dec 18 2006 - 12:47:01 CST

Thank you for explaining that to me.

While I trying to calculate the surface tension of my system using NPAT simulation, I have the following questions:


1) Should not the summation of the nine components of the pressure tensor give the reported instantaneous pressure in the log file? They do not match in my case.

2) According to Zhang et al. 1995, the Pzz should be close if not the same as the (LangevinPistonTarget   1.01325). I have set (LangevinPistonPeriod   200.0, LangevinPistonDecay    500.0) and I the Pzz is not close to the applied pressure, is there any thing wrong about that?

3) I had my system with NPgT using (SurfaceTensionTarget   46.0) , then I switch to NPAT and by using Feller et al equation Gamma = <Lz(Pzz - 0.5(Pxx + Pyy)>, the value I got is var away from 46, I do not know if the the two methods use different ways for the surface tension or Pzz, Pxx, and Pyy from instantaneous pressure in the log file are not right.


I appreciate any help about these issues.

Thanks

Morad Alawneh






JC Gumbart wrote:
That is the pressure tensor (Pxx Pxy Pxz etc.).  Since these values fluctuate a lot, only averages are meaningful though.  All off-diagonal values should average to zero, as one would expect, leaving the pressure along each dimension only.

On Dec 15, 2006, at 8:50 PM, Morad Alawneh wrote:

Dear NAMD users,

When activating the option outputPressure with a value of 100 it will print out on the log file the atomic and group pressure tensors.

This is an example:

PRESSURE: 100 453.842 -196.671 -654.667 -113.111 109.92 321.118 -729.011 328.808 -58.3356

I know the first number corresponds to the time step, but my question is

what is the meaning of the other 9 numbers?

Thanks

Morad Alawneh

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