[gmx-users] Questions about free energy calculation tutorial
gozdeeergin at gmail.com
Sun Nov 6 14:27:50 CET 2016
> If it's the salt, then take the known Na+ value for the force field and add it to the SDS value you obtain at infinite dilution. Straightforward.
Ok either I can take hydration free energy of Na from the literature or I can run 2 thermodynamic integration with dodecyl sulfate and Na separately and sum them.
Besides this I would like ask how did you manage the get the very similar solvation free energy result with experiments without adding Coulomb interaction which means decoupling only the L-J?
Do you think to estimate the correct solvation free energy for dodecyl sufate(-) and Na(+) I need to decouple also the Coulombic interaction?
If yes, in order to do that I just need to modify the coul_lambdas parameter in .mdp file, right?
Also I should not make the charge of the atoms as zero in topology file.
According to the Sander Pronk tutorial of Solvation free energy of ethanol, I can turn off both the electrostatic (Coulomb) interactions and the Van der Waals (Lennard-Jones) interactions at the same time.
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