[gmx-users] analysis of PMF calculations

Justin A. Lemkul jalemkul at vt.edu
Sun Sep 11 21:50:16 CEST 2011

Rebeca García Fandiño wrote:
>  Hello,
>  I have some old calculations (Umbrella Sampling) carried with Gromacs 
> 3.3.3 and I would like to analyze them using Gromacs 4.
>  When I use:
> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 
> -max 2.4750 -o pmf_1_cycl.xvg -hist histogram_cycl.xvg -ip 
> ./pdo-files.dat -cycl yes
> I get a curve with no errors, however if I don't use the option "-cycl yes"

FYI, this syntax is wrong.  Boolean options are -cycl/-nocycl.  They do not take 

> /GROMACS/4.5/32/bin/g_wham -bins 100 -temp 300 -tol 0.0001 -min -2.4750 
> -max 2.4750 -o pmf_1_no_cycl.xvg -hist histogram_no_cycl.xvg -ip 
> ./pdo-files.dat
> I get a profile where the second column is all "zero"

That makes sense.  You're telling g_wham that you have a PMF starting and ending 
at the same place, but it's not a periodic profile.  It can't debias the 
sampling windows over zero space.

> The last lines of the analysis are (just in case it helps...):
> (...)
>     54700) Maximum change 1.204571e-02
>     54800) Maximum change 1.318242e-02
>     54900) Maximum change 1.235132e-02
>     55000) Maximum change 1.802996e-02
>     55100) Maximum change 1.166826e+00
>     55200) Maximum change inf
>     55300) Maximum change 3.161195e-01
>     55400) Maximum change 3.437561e-01
>     55500) Maximum change inf
> Switched to exact iteration in iteration 55501
> Converged in 55508 iterations. Final maximum change 0
> I have tried to change to use the option "auto" to determine min and max 
> automatically, I have also tried to remove the tolerance (and set the 
> default), but the result was the same, I always obtain zero in the 
> second column without the option -cycl yes.

Again, this would be incorrect syntax.  The option "-cycl auto" does not exist.

> Does anybody have any idea of what is happening? Why the second column 
> in the PMF profile is set to zero?

See above.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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