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