From: Nicolas Sapay (n.sapay_at_ibcp.fr)
Date: Mon Aug 29 2005 - 07:12:27 CDT
Hello everybody.
I have performed the simulation of a peptide in a POPC membrane at
constant pressure and temperature with unable wrapping and cell
flexibility. Now, I want to compute the nonbonded contribution to the
pressure profile. I have then re-centered my cell on the POPC CoM and
compute the pressure profile as following :
Plateral -Pnormal = (Pxx + Pyy)/2 - Pzz
The profile is consistent with the literature (Lindhal & Edholm, 2000)
but the standard variation is incredibly high for z coordinates beyond
the glycerol-C=0 moiety (roughly +/- 1200 bar). Is someone ever met this
problem? Is this can be due to the electrostatic energy computation? In
fact, PME doesn't seem to be implemented with the nonbonded component
computation. I have then use a more important cutoff (20 A).
Thanks for your answers
Nicolas Sapay
--
_ Nicolas Sapay ____________________________________________
Ph.D sudent in structural bioinformatics
Institut de Biologie et Chimie des Proteines
CNRS - Claude Bernard University, Lyon I
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