Re: Pressure Profile Simulation

From: Nicolas Sapay (
Date: Thu Aug 25 2005 - 04:32:40 CDT

Dear Yong,
You are right about the computation of nonbonded component in the
pressure profile. Additionally, you have to disable the PME calculation
and then use a long nonbonded cutoff.
Additionally, I also have a question to the NAMD community. I am trying
to compute the pressure profile along the normal to a POPC bilayer. The
simulation has been compute with wrapall "on" and COMmotion "no" at
constant pressure and temperature.Consequently, the COM of the membrane
moves around the z axis. How the pressure profile computation takes into
account this motion? Should I systematically re-center my system on the
membrane COM?

Thanks a lot!

Nicolas Sapay
Le jeu 25/08/2005 à 04:36, Gan, Yong (UMC-Student) a écrit :
> Hello, Dear All:
> I have one question about the pressure profile calculations.
> According to my understanding, the method to get the pressure profile has two steps. First, conduct the MD simulation to obtain the pressure profile without the nonbonded term; Secondly, use
> the DCD file and Tcl script to get the nonbonded term only; Last, the sum of the above two results is the desired pressure profile. It it right?
> Thanks a lot!
> Yong

_ Nicolas Sapay ____________________________________________
  Ph.D sudent in structural bioinformatics
  Institut de Biologie et Chimie des Proteines
  CNRS - Claude Bernard University, Lyon I
  > contact :
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