[gmx-users] Calculation for PMF, Wham error

[Justin Lemkul]

On 10/17/19 2:09 PM, Rabeta Yeasmin wrote:
> 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?

Usually this means you have no sampling in that region of the reaction 
coordinate. Check your histograms.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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