VMD-L Mailing List

From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Tue Feb 19 2019 - 10:34:03 CST

Hi Brian,

Thank you for the response. I went back and re-ran both calculations with
the default temperature in the GUI (300 in both cases).

Version 1.9.3
300 K: total free energy change is -89.32071464053809 , total error is
0.09901395668211348
310 K: total free energy change is -89.32071464053809 , total error is
0.09901395668211348

Version 2.1
300 K: total free energy change is -98.6952146581652 , total error is
0.063764981495484
310 K: total free energy change is -98.7037132059109 , total error is
0.07093475906066159

The older version does not seem to accept the temperature change, as you
suggested, while version 2.1 gives a slightly different result with the
higher temperature provided. Should I take the result from version 2.1 to
be the more reliable one? I am also sending my fepout files to Jerome
off-list for further evaluation of this difference.

Thank you,
Amy

On Mon, Feb 18, 2019 at 4:31 PM Brian Radak <brian.radak_at_gmail.com> wrote:

> 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
>>
> 

-- 
Amy Rice
Ph.D. Candidate
Physics Department
Illinois Institute of Technology