Dear GROMACS users,<br><br> As another check, I simulated the hydration of Sodium ion. The results for the free energy change of un-charging the sodium ion with ffG43a1 force field parameter from q=+e to q=0 in SPC water are the following:<br>
<br> 363.3 +/- 2.4 kJ/mol in GROMACS 4.0.7<br> 404.7 +/- 1.9 kJ/mol in GROMACS 4.5.3<br> 405.2 +/- 2.0 kJ/mol in J. Phys. Chem. 1996, 100, 1206-1215,
Table 5<br><br> Again there is difference between the results from 4.0.7 and 4.5.3.<br><br> It seems that the problem might be related to the net charge of the system. In both cases of Cl- and Na+, the system contains 1 charged ion and certain number of water molecules. Is there any change of the GROMACS codes dealing with Coulomb interaction in free energy calculation from 4.0.7 to 4.5.3?<br>
<br> Thanks!<br><br> Yan<br><br><br>