[gmx-users] Different TI free energy values in 4.0.7 and 4.5.3

Yan Chai chai.yan.em at googlemail.com
Fri Apr 15 09:25:26 CEST 2011

Dear GROMACS users,

  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:

  363.3 +/- 2.4 kJ/mol    in   GROMACS 4.0.7
  404.7 +/- 1.9 kJ/mol    in   GROMACS 4.5.3
  405.2 +/- 2.0 kJ/mol    in   J. Phys. Chem. 1996, 100, 1206-1215, Table 5

   Again there is difference between the results from 4.0.7 and 4.5.3.

   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


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