[gmx-users] analysis of PMF calculations

Rebeca García Fandiño regafan at hotmail.com
Sun Sep 11 21:29:57 CEST 2011

 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"

/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"

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

Thanks a lot for your help in advance.

Dr. Rebeca Garcia
Postdoctoral student
Santiago de Compostela University
regafan at hotmail.com
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