[gmx-users] umbrella sampling

Erik Marklund erik.marklund at chem.ox.ac.uk
Sun Sep 21 16:02:59 CEST 2014


Three coordinates and a reference make a three dimensional distance, which is your reaction coordinate. Simple as that.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 21 Sep 2014, at 11:39, susanta haldar <susantahaldar at gmail.com> wrote:

> Hi all,
>  I am running a umbrella sampling simulation. Pulling a lysine residue
> near to inhibitor inside a protein. So that I used pull code in 3 dimension
> (pull_dim = Y Y Y ). Therefore I got 3 coordinates (dx, dy, dz) in the
> pullx-file.xvg. Now I need to run g_wham to calculated the PMF.
>   How the WHAM would be working here? How to work with all those 3
> coordinates to calculate the Free energy of pulling?
> I would be very happy if somebody help me on this regard.
> thank you in advanced.
> -- 
> Susanta Haldar
> Institute of Organic Chemistry and Biochemistry
> Academy of Sciences of the Czech Republic.
> -- 
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