From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Thu Jan 14 2010 - 05:00:18 CST
Branko,
In my experience, typical 2D grids require at least a few million
steps for convergence (which should still run fairly quickly). Even
simpler, if you don't specify the number of steps, the program will
try to run until convergence, as explained in the manual. It can be
useful to start off with a higher hill height parameter (maybe 0.05
kcal/mol) to quickly obtain a slightly coarser PMF. Note that
integrating PMFs in dimension higher than 2 is somewhat more involved.
Also, I strongly recommend that you use the updated version of the
code from NAMD CVS (I am attaching it for convenience). It uses a
different choice of boundary conditions (regions not-sampled in the
ABF run are now excluded), which gives more consistent results for
poorly-sampled gradient fields.
By the way, what did you have to do to make the program work?
Best
Jerome
2010/1/14 Branko <bdrakuli_at_chem.bg.ac.yu>:
> Jerome,
>
> With the little help of my friends skilled in programming abf_integrate is
> now fictional, but when one use different number of MC steps (10000 vs.
> 2000000) resulted free energy surfaces are entirely different. All other
> parameters are holding on default –t 500 –m 1 –h 0.01 –f 0.5. Please advise
> me how rationally and reasonably to choose number of steps to obtain
> realistic results. Thanks a lot in advance.
>
> Branko
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