[gmx-users] g_bar ... the right answer for the wrong reason?

[Justin A. Lemkul]

On 6/28/12 11:17 AM, Michael Brunsteiner wrote:
>
> so i do:
> git clone git://git.gromacs.org/gromacs.git (which i understand gives me
> gmx-4.5.5+bug fixes)
>

Not entirely - this clones the master branch.  I don't believe the 4.6 free 
energy changes have been merged in, so you've basically using 4.5.5 with some 
other stuff changed.

You need to

git checkout --track -b release-4-6 origin/release-4-6

to access the 4.6 code with free energy changes merged.  I don't know whether 
everything is functional at this point, and I believe mdrun has some performance 
issues because not all changes have been completed.

> g_bar_d -f mdv*.xvg -b 100    ; this is Program g_bar_d, VERSION
> 5.0-dev-20120628-b4320dc
> [...]
> WARNING: Some of these results violate the Second Law of Thermodynamics:
>           This is can be the result of severe undersampling, or (more likely)
>           there is something wrong with the simulations.
> [...]
> total   0.000 -  1.000,   DG -9.00 +/-  0.15
>
>
>
> and with the original gmx-4.5.5
>
> g_bar_d -f mdv*.xvg -b 100  ; this is Program g_bar_d, VERSION 4.5.5
> [...]
> WARNING: Some of these results violate the Second Law of Thermodynamics:
>           This is can be the result of severe undersampling, or (more likely)
>           there is something wrong with the simulations.
> [...]
> total   0.000 -  1.000,   DG -8.05 +/-  0.62
>
> this is for turning off VdW. the result fromt the runs in which i turn off the
> charges only
> are the same in both cases ...
> the input data is the same, the two results differ by more than the error-bars
> question is, which one correct, and the warning, which i see in both cases, do i
> want to take it serious?
>

I'd try to base a conclusion using the release-4-6 branch.

-Justin

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

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

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