[gmx-users] Calculation for PMF, Wham error

Rabeta Yeasmin rabetayeasmin at gmail.com
Thu Oct 17 20:09:02 CEST 2019


Dear GROMACS users,

I am a new user of GROMACS. I am trying to calculate PMF for the
translocation process of a protein through lipid bilayer. I have set up
total 61 windows above and below the lipid bilayer with a gap of 2A and run
umbrella sampling simulation for 100ns, using a force constant of 3
kcal/mol.A2. But after trying to combine results in wahm, I am getting
something like this-

-5.901639e+01   -nan
-5.704918e+01   -nan
-5.508197e+01   -nan
-5.311475e+01   -nan
No PMF value is showing for the windows. I am using the following command
to run wham-

gmx_mpi wham -it tpr-files.dat -if pullf-files.dat -bins 61 -temp 313.15
-min -60 -max 60 -o -hist -unit kCal

Can anyone please help me why I am getting this kind of error?

Thanks.
Rabeta Yeasmin


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