[gmx-users] Use g_wham on 2D PMF

XAvier Periole x.periole at rug.nl
Tue Feb 4 10:56:52 CET 2014

g_wham does only 1D PMF but can handle several restrains. 

There is 2D code on Alan Grossfield website. Plumed refers to it. 

On Feb 3, 2014, at 5:54 PM, "DAI, JIAN" <jdai2 at fsu.edu> wrote:

> Dear all:
> Is it possible for g_wham to calculate 2D PMF? 
> It seems to me that g_wham can deal with this because the example for the pdo files in the g_wham documentation has two groups and it says that it can handle up to four pull groups.
> Say I have a bunch of time series for two variables in different folders, and after running g_wham using the -ip option I got histo.xvg and profile.xvg, but neither of these two seems to contain information of a free energy landscape. Do I miss something?
> Another question: Using wham-2d we are able to get the free energy landscape. We also want to do bootstrap analysis of the variation range of the 2D PMF, but I'm not sure how to do that? Naively I thought of generating bootstrap sample for each window, do WHAM-2d and calculate the variation. Is this correct?
> Thank you.
> Jian
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