VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Feb 18 2019 - 16:31:07 CST

Hi Amy,

I've noticed this also. I believe there were some bugs in the BAR estimator
(and fepout file parsing) that were addressed between 1.9 and 2.1. I'm
surprised that the magnitude of difference is so large, but it's quite
reasonable that they are different.

Older versions also have some problems with modifying temperature from the
GUI (they get "stuck" at the default 298 K). Please double check and run
the calculation with the default settings and then change to 310 K to make
sure this is properly working. If the result doesn't change, then there is
likely a bug.

Brian

On Mon, Feb 18, 2019 at 4:48 PM Amy Rice <arice3_at_hawk.iit.edu> wrote:

> Hi all,
> I noticed that using different versions of ParseFEP (1.9.2 vs 2.1) gives
> different free energy output when supplied with the same fepout files and
> temperature selection. With 1.9.2, the free energy change was calculated as
> -89.320 with a total error of 0.099. The same files in version 2.1 resulted
> in a free energy change of -98.704 and a total error of 0.071. Is this
> expected behavior? In both cases, I set the temperature to 310 K and
> selected to use the BAR-estimator method. Was there a change in how the
> calculation is performed between these two versions? It is a little
> disconcerting to have such a large difference between the two. I have
> attached the log file for both cases.
>
> Best,
> Amy
>
> --
> Amy Rice
> Ph.D. Candidate
> Physics Department
> Illinois Institute of Technology
>