ABF simulations

From: Sumanth Jamadagni (jamads_at_rpi.edu)
Date: Tue Jun 09 2009 - 21:08:10 CDT

Dear NAMD users,

We have been trying to run some simple ABF simulations to calculate to
PMF along z between a molecule and a surface (or similar systems, we
have faced the same problem).
The problem is this: we specify an /ximax/ and /ximin/ for the reaction
coordinate. The center of mass of the molecule initially samples the
reaction cordinate and then the molecule is stuck at one end of the
reaction coordinate (ximax or ximin) and doesn't diffuse and sample the
whole range any more. It therefore accumulates statistics only in the
first or last few bins, and there are very few statistics in the rest of
the bins. I will try running the sims for much longer to see if that
helps, but I suspect I am missing something.

Thanks
Sumanth Jamadagni

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