[gmx-users] umbrella sampling
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.
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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