[gmx-users] Charged wall

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Nov 11 16:48:27 CET 2011

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:



-- 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


More information about the gromacs.org_gmx-users mailing list