[gmx-users] Questions about free energy calculation tutorial
gozdeeergin at gmail.com
Sun Nov 6 13:38:40 CET 2016
> If you need the total free energy of hydration for NaSDS, you can just decouple SDS in water with no Na+ and sum the two contributions (SDS and Na+ separately). If you just want the SDS hydration free energy, decouple it in a box of pure water
I have difficulty to understand NaSDS? SDS is Sodium dodecyl sulfate so Na is in this molecule.
What about running the simulation with both Na ions and dodecyl sulfate inside the water. However I just decouple the dodecyl sulfate part.
I also make the charge of Na ions zero so I can run the simulation with net 0 (zero) charge.
Na ions will physically be there but their charge will be zero.
Is not this more closer to experimental SDS hydration state?
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