Re: Umbrella Sampling Methodology

From: Charlie Forde (
Date: Wed Aug 18 2010 - 11:39:17 CDT

Dear Dr. Fiorin,

Thank you for your reply.

You wrote: “I suppose the protein is held fixed by position restraints?”
In a sense yes.

I will attach the upper atoms of the surface to a lower fixed set of atoms (through the use of the keywords fixedAtoms, fixedAtomsFile and fixedAtomsCol in the .conf file). The upper surface atoms are not expected to undergo much if any reorganization, the distance of the surface to the center of mass of the molecule will thus depend on the molecule and not the surface. I understand that if I didn't fix the lower set of surface atoms then the Group2 selection would have to comprise a group of surface atoms rather than a dummyAtom, nevertheless it may be beneficial to make this change to Group2, which in turn would necessitate the inclusion of a second centers value.

Is it correct to say that in this instance, the value of the centers is the magnitude of the position vector for each of the two centers of mass?

Thank you for highlighting the histogram and width keywords which I was unaware of, for the moment however, until I gain more experience with the method, I will not use them.



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