[gmx-users] Query on WHAM analysis

chris.neale at utoronto.ca chris.neale at utoronto.ca
Mon Jun 21 07:35:08 CEST 2010

loc_win_min is the center of restraint
spring is the force constant in kcal/mol (1000kJ/mol/nm^2 /4.184 = x  

You should probably read the manual again, this stuff is all there.

I'll not answer any further questions on this as (1) it's in Alan's  
manual, and (2) this list is not really the appropriate place for a  
question on AG's wham.


--- original message ---

Hi all,

I am doing the umbrella sampling of a ligand pathway (Gromacs4.0.4).Now i
want to plot the PMF using WHAM analysis by Alan Grossfield. I installed the
WHAM program, read the manual too. But i am confused with the "loc_win_min"
and "spring" terms in the metadata file.

Can anyone please explain me these two terms?

I have the pullx files from 21 umbrella samplings.(I guess this will go as
the first term in the meta data file.).
Pull_k1 used for Us was 1000.

Please let me know if you need any other details.

Thanks in advance,

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