new NAMD user ABF setup question

From: Elio Cino (ecino_at_uwo.ca)
Date: Thu May 27 2010 - 14:10:04 CDT

Hello. I have been trying to calculate free energies of peptide binding to a protein with umbrella sampling in gromacs with mixed results. Anyways, I was hoping the ABF method may help me get accurate results faster than umbrella sampling. I have read some of the ABF tutorial and manual, but am a bit confused about the ABF setup. I set the boundaries for the COM distance between the peptide and protein, but I think I need to specify a direction also since I want to pull the peptide away from the protein along a specific coordinate. I am unsure if they is correct, and if so how to specify the direction. Also, I read a comment saying that much of the ABF calculation time is spent climbing uphill to overcome the forces (between peptide and protein) at low COM distances and to avoid this, the lower boundary should be increased. Will this still provide an accurate PMF? It seems that excluding these low boundary states would cause some errors in the delta G. Any help is appreciated. Thanks. 

Elio Cino

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