From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Aug 25 2005 - 18:00:25 CDT
There isn't any code to identify the membrane location so, yes, you would
need to re-center the system on the membrane for every frame in your
simulation (which should be straightforward to script using VMD).
On Thu, 25 Aug 2005, Nicolas Sapay wrote:
> 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!
> _ Nicolas Sapay ____________________________________________
> Ph.D sudent in structural bioinformatics
> Institut de Biologie et Chimie des Proteines
> CNRS - Claude Bernard University, Lyon I
> > contact :
> 7, Passage du Vercors Tel: +33 (0)4 72 72 26 46
> 69367-F Lyon cedex 07 Fax: +33 (0)4 72 72 26 04
> France Web: http://pbil.ibcp.fr/
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