Hi gmx-users, I'm trying to simulate a umbrella sampling PMF between two benzene molecules in vacuum. My protocol is working fine, my histograms have good overlap and the curves I have got are quite reasonable.
However I have noticed that some options in my .mdp file can significantly change the depth of the well. Also the curves can not go to zero at long distances. For example, if I use PBC I get a reasonably good value for the minimum of the PMF but from a certain separation it starts to increase slightly in a linear fashion instead of going to zero. On the other hand, if I make pbc = no, I get an acceptable curve, with the PMF going to zero, but with the minimum too high. Someone could give me any tips on the best set of parameters to calculate this PMF in a vacuum? bests eef _______________________________________ Eudes Eterno Fileti Centro de Ciências Naturais e Humanas Universidade Federal do ABC — CCNH Av. dos Estados, 5001 Santo André - SP - Brasil CEP 09210-971 +55.11.4996-0196 http://fileti.ufabc.edu.br
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