[gmx-users] Position restraint file

Bob Johnson robertjo at physics.upenn.edu
Thu Aug 11 22:00:24 CEST 2005

I am studying the interactions between single stranded DNA and a carbon
nanotube. I am using the Amber force field for the DNA molecule. When the two
systems (dna and nanotube) are brought together, the nanotube is severely
deformed by the presence of the dna. I wanted to try restraining the positions
of the nanotube since it is probable that the nanotube structure remains the
same upon insertion of a dna molecule. How would I format the posre.itp file?
Do I specify the coordinates of all the nanotube carbon atoms along with a
force constant? I'm unsure of the syntax.
Bob Johnson

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