Re: rough edges of energy landscape when running ABF

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Thu Jun 10 2010 - 12:04:14 CDT

Hello Crick, you can look at the samples profile, <jobname>.count, and see
whether the number of samples in the region you mention of the pmf is
particularly low. Most likely, there is not enough statistics for those
regions and the average force has not been computed accurately yet.

Giacomo

---- ----
 Dr. Giacomo Fiorin
 ICMS - Institute for Computational Molecular Science - Temple University
 1900 N 12 th Street, Philadelphia, PA 19122
 giacomo.fiorin_at_temple.edu
---- ----

2010/6/10 crazylyf <crazylyf_at_163.com>

> Hi everyone,
>
> When I plot the phi and psi free energy landscape as the tutorial says, I
> get a picture basically correct but with rough edges between different
> areas. Was it caused by non-equilibrated system or insufficient energy
> output?
>
> Thanks,
>
> Crick
>
>
>
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