From: Giovanni Bellesia (giovanni.bellesia_at_gmail.com)
Date: Fri Apr 08 2011 - 09:48:50 CDT
I have a small protein "sitting" on a solid surface made up by cellulose
chains and I would like
my protein to "explore" a small portion of the surface itself.
The idea is use ABF (and/or metadynamics) to generate a
2D free energy map to find out which "spots" on the cellulose surface
correspond to free energy minima.
I was wondering if anyone has suggestions in terms of choice of a pair of
suitable collective variables.
In more detail, I was wondering how to choose a pair of cvars in a way that
the ABF (or metadynamics) calculation drives the protein
to "move" on the surface without "taking off" and moving back in the bulk
water topping the surface.
The protein surface interaction is hydrophobic in nature and in my starting
the hydrophobic groups in my protein are already in contact with the
All this to say that I don't need to explore possible alternative
I just need the protein to simply "slide" on the surface with the same
relative orientation (i.e. hydrophobic groups in contact with the surface).
Thanks for your help
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