**From:** Jerome Henin (*jhenin_at_cmm.chem.upenn.edu*)

**Date:** Mon Nov 19 2007 - 15:56:17 CST

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Jancong,

If I were you, before starting such a calculation, I would get a feel

for the technical issues involved by trying to run a "small", "easy"

ABF calculation, such as the acetate-guanidinium ion pair that we

describe in the reference paper of NAMD's ABF implementation.

I don't think the "brute-force" approach will work here. In

particular, the orientational averaging would not work. It would

probably be possible to sample a particular dimerization pathway by

enforcing orientational restraints (see e.g. the acetate-guanidinium

case).

Is the interaction *free energy* along a dimerization pathway really

what you are interested in? There should be means to estimate the

interaction energy in the dimer through "standard" simulations,

although I have never thought about the specifics. Anyway, that would

be easier to obtain and probably easier to interpret, as well.

Jerome

On Nov 19, 2007 3:33 PM, jia <jia_at_ornl.gov> wrote:

*> Dear NAMD users and Jerome,
*

*>
*

*> I'm trying to use ABF method to calculate the binding energy of two small size
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*> proteins, 140 a.a for one and 57 for another, and I'm wondering if it's a good
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*> idea to choose the reaction coordinate as the distance separating the centers
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*> of mass of these two domains given the fact that many atoms will be
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*> participating to the center of mass. Any suggestions will be appreciated.
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*> Thanks much!
*

*>
*

*> Jiancong
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*>
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*> Postdoc Research fellow
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*> Center for Molecular Biophysics,
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*> Oak Ridge National Lab
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*> Oak Ridge, TN, 37830
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*>
*

*>
*

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