[gmx-users] 2D PMF for two ions

Rebeca García Fandiño regafan at hotmail.com
Mon May 12 13:26:36 CEST 2014

I am trying to carry out a 2D PMF calculations of two ions in a peptidic channel using GROMACS (and Umbrella Sampling). 
I have several technical questions:
-Should I consider pull_ngroups    = 3 (two of them ions and the other one the channel)? 
 should I carry out a 1D PMF for one of the ions (leaving the other ion 
free), and then doing the same for the other ion and combine the 
results? In that case is there any tool for combining the results 
obtained for both ions? I have seen 2d-wham, but it is not implemented in GROMACS, is it? 
Thanks a lot in advance.

Dr. Rebeca Garcia
Santiago de Compostela University

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