[gmx-users] mdrun_hole

[Xavier Periole]

Hy Jose,

I was just about writing to you to tell how good it worked for
my protein insertion in the membrane. The only bad point was to
go back to the gmx2.0 version, which was already installed on
our system, so not a big deal.
This procedure must definitly inserted in the gromacs package.

The only thing I would change is the way erase the lipids inside
the protein volume, and the water. What we have done here is
to select the phosphorus inside the volume of the protein using
their circular variance. We did the same with the water molecules
and the result is that you need only 5 ps with the first force value
(1 kJ.mol-1.A-1) and another 5 ps with the second force value
(10 kJ.mol-1.A-1). After taht I equilibrated the water (100ps) and
the lipids (200ps) with the protein fixed. I worked really well.

Xavier

Department of Physiology and Biophysics
Mount Sinai School of Medicine - NYU
New York, NY 10029