VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Mon Dec 08 2008 - 13:25:30 CST

Dear all,

I have been observing some bizarre behavior while trying to equilibrate a
patch of membrane, and I am wondering if anyone has seen similar things, and
might tell me what I am doing wrong.

Starting with long skinny patch of membrane created my replicating a smaller
pre-equilibrated piece, I follow an elaborate minimization, restraining the
lipids and running conjugate gradient while reducing the strength of the
restraints. after about 20k conjugate gradient steps, the system is
unrestrained and the gradient is below 1. I then heat to 310 via
reassignment, and then run a few thousand steps at constant pressure with
velocity rescaling every 100 steps. at this point, the membrane begins to
'delaminate'---the two leaflets start two peel apart. eventually the two
leaflets bulge away from each other, leaving a cylindrical void. the void is
vacuum--no solvent, etc.

weird. any thoughts?

Thx,
Ed