<div>Hi gmx-users, </div><div>I have tried to calculate the free energy of transfer of </div><div>a solute between two solvents by thermodynamic integration. </div><div>However, the dgdl plot I have obtained is not smooth enough to ensure accuracy. </div>
<div>I have used a non homogeneous spacing for lambda. The first is from 0.0 to 0.4 (dl=0.04),</div><div>the second is from 0.405 to 0.48 (dl=0.005) and the third is from 0.48 to 1 (dl=0.04). </div><div>Overall, I was performed 40 simulations.</div>
<div>As can be seen in the figure ( <a href="http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg">http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg</a> ), </div><div>there is a large fluctuation in the region that goes from 0.40 to 0.48. </div>
<div>Each simulation was carried out by 0.5ns preceded by 0.15ns of equilibration. </div><div>I am using soft-core whose parameters are:</div><div><br></div><div>; Free energy control stuff</div><div>free_energy = yes</div>
<div>init_lambda = 0.00</div><div>delta_lambda = 0</div><div>sc_alpha = 1.3</div><div>sc-power = 1.0 (for this I also used 2).</div><div>sc-sigma = 0.47</div>
<div><br></div><div>In the example of the link sc-power=1, but I re-did the calculations with sc-power=1 </div><div>and I found the same behavior (although the format of the plot was a little different). </div><div><br></div>
<div>Can you suggest me a way to calculate this free energy difference with accuracy? </div><div>The perturbation free energy method could give better results? </div><div><br></div><div>Thank you </div><div>EEF</div>_______________________________________<br>
Eudes Eterno Fileti<br>Centro de Ciências Naturais e Humanas<br>Universidade Federal do ABC<br>Rua Santa Adélia, 166 - Bloco B, Sala 1048<br>09210-170 Santo André - SP Brasil<br>+55.11.4437-8408<br>skype: eefileti<br><a href="http://cromo.ufabc.edu.br/~fileti/">http://cromo.ufabc.edu.br/~fileti/</a><br>