ABF question

From: Xu, Jiancong (xuj1_at_ornl.gov)
Date: Wed Jan 09 2008 - 10:04:19 CST

Hi All,

I'm performing an ABF calculations with the reaction coordinate spanning between 20 and 30 A defined by "distance-com". The reaction coordinate was split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about 100ps long, no single data point fell into the 25-30 A range. Does this mean the default force constant applied at the borders of the reaction coordinate (10 kcal/mol/A2) is too small?

I'm also wondering if there's any ABF tutorial available on NAMD website with all the input files for a model system. That'd be greatly helpful.


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