[gmx-users] Question about g_bar output

Justin A. Lemkul jalemkul at vt.edu
Wed Jun 29 21:33:57 CEST 2011



Warren Gallin wrote:
> Justin,
> 
> 	OK, this makes sense to me, and I can do the interconversion of units easily enough outside of the GROMACS tools.
> 
> 	Should I file a bug report?
> 

No need.  I've fixed this in the release-4-5-patches branch so the output will 
be correct whenever version 4.5.5 is released.

-Justin

> Warren Gallin
> 
> On 2011-06-29, at 12:48 PM, Justin A. Lemkul wrote:
> 
>>
>> Warren Gallin wrote:
>>> Hi,
>>> 	I've just run g_bar on data from a simulation, and I am having trouble reconciling the graphical output with the numerical output.  The units seem to be inconsistent.
>>> 	In particular the numbers under detailed results are in units of kT, followed by final results in kJ/mole (see below).
>>> 	However, the graphical output from -o and -oi seem to numerically be from the kT units list, but the y-axis is labelled in kJ/mole (see atached PDF files.
>>> 	Am I missing something here, or is this a bug in the output code?
>> There is a bug.  Proper output is discussed in the BAR tutorial:
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/07_analysis.html
>>
>> -Justin
>>
>> -- 
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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