From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Wed Jan 09 2008 - 11:26:57 CST
It is best to prepare an equilibrated system with the RC in the
desired range, using any kind of appropriate restraints. The boundary
biases of ABF are harmonic - if you start far away from the min or max
value, the excessive pulling on the system may have side-effects.
An ABF tutorial is in preparation. We will announce it on this mailing
list when it goes online - this should not take very long.
On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1_at_ornl.gov> wrote:
> 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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