From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Apr 08 2011 - 11:21:33 CDT
Hello Giovanni, I think Cartesian coordinates of the protein's center of
mass can be used as collective variables, and should be also very intuitive
to analyze. Use a distanceZ-based colvar in all three cases, redefining the
"axis" each time. Along x and y (surface-parallel) you may want to define
their period, to take advantage of the periodic boundary conditions. To
prevent the protein from coming off, you can set a boundary potential along
z, which doesn't kick in within a tolerance distance of your choice: this
way the protein can be free to jump over the corrugations of the surface,
but not come off it permanently.
Giacomo Fiorin - Postdoctoral Researcher
ICMS - Institute for Computational Molecular Science - Temple University
1900 N 12 th Street, Philadelphia, PA 19122
On Fri, Apr 8, 2011 at 10:48 AM, Giovanni Bellesia <
> Hi all,
> 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
> protein-surface contacts.
> 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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