You could create an atomistic charged wall by placing atoms in a plane
or grid and using position restraints or freeze groups to keep them in
place. You could them use the pull code to restrain part of the
protein relative to an atom(s) in this atomistic wall. You could
obtain your desired charge distribution by using a combination of
helium and sodium or chloride atoms. Alternatively, you could create a
new atom type with a fractional charge and whatever LJ parameters you
want. Of course, you could also construct a more atomistically
realistic wall.Some people have done similar things to study proteins
absorbed onto electrodes:
http://pubs.acs.org/doi/abs/10.1021/ja910707r
http://www.sciencedirect.com/science/article/pii/S0013468609003119
Chris.
-- original message --
Hi Gmx Users,
I am wondering whether is it possible in Gromacs to build sth like a
charged wall to which the last residue of my terminal protein will be
attached and run the simulation? I mean that the protein cannot move
through some border which is attached to and which is positively or
negatively charged.
Thank you
Steven
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