Membrane Protein Simulation Problems

From: Ilya Chorny (
Date: Fri Oct 12 2007 - 22:31:28 CDT

Dear Richard,

I got your contact info from the NAMD mailing list. I am a member of the
Stroud Lab at UC San Francisco and I am working on a membrane protein
simulation. I am having some trouble with my protein. I prepare my
simulation box by inserting the protein into the membrane, deleting
overlapping lipids, solvating the system and adding counter ions. I minimize
and then equilibrate the system for 2 ns. In the initial 2 ns simulation I
fix the position of protein atoms and constrain the lipid phosphates in the
Z dimension (along the pore axis). I then run an 8ns simulation in which I
release the constraints on the lipid and constrain the CA positions of the
protein. After my 10 ns equilibration I run another 8 ns simulation in which
the whole system is free. In the last 8 ns simulation my protein seems to be
falling apart. The RMSD keeps increasing and the channel residues which
should be fairly constrained move all over the place. I monitor my
equilibration by calculating the protein-lipid energy which seems to have
converged. Any ideas on what I can do to debug my problem? The membrane is



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