Protein in a Lipid Membrane

From: Ale Gomez (
Date: Thu Jun 10 2010 - 05:22:33 CDT

Hi everyone
I am working on a system with a protein in a lipid membrane. My system has
almost 40 thousand atoms and measures 75X75. I had a lot of problems
preparing the equilibration conf file because it doesn't run (my system
became unstable or has atoms moving too fast) unless I use the following

# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 22.
switching on
switchdist 18.
pairlistdist 24.5
margin 1.5

# Integrator Parameters
timestep 0.1 ;# 2fs/step
rigidBonds none ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20

Comparing with the parameters in membrane tutorial (available in NAMD
website), my numbers are bigger and I do not know if these are correct.
Could any one help me with this predicament??.
Thanks in advance!!.
Ale Gómez
Biophysics and Molecular Modeling Group
Physics Department
Escuela Politécnica Nacional, Quito - Ecuador
Ladrón de Guevara E11-253.
Casilla 17-01-1253

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