peptides confined in a water sphere

From: Giovanni Bellesia (
Date: Thu Jan 19 2006 - 09:37:01 CST

I'd like to study the dimerization process of two small peptides in
I want to confine them within a sphere to try and speed up the process
and, at the same time, to mimic some "external confinement".
Obviously i can use the spherical harmonic conditions but i was
thinking about
using PBC (two peptides in a water box) to avoid the artifacts related
to water dynamics at the water-vacuum interface.
Nevertheless I need to confine (ONLY) the motion of the two peptides
into a sphere using something quite similar to the potential used by
namd in spherical boundary conditions

Any suggestions ?



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