[gmx-users] Calculating enthalpies of solvation.
wwelch000 at gmail.com
Fri Mar 8 21:22:34 CET 2019
I want to obtain values for enthalpies of solvation of nucleotide
phosphates. My initial idea was to calculate values for the solvated
system, the waterbox without the molecule, and the gas phase molecule.
Enthalpies are only calculated using the NPT ensemble, so I was thinking
that for the gas phase molecule, I could just use a huge box with a
pressure of .001 atm and the cutoff scheme for coulombic interactions with
a radius that exceeds the size of the molecule. I'm running such
calculations on AMP and they work, but it seems that the enthalpy value I
get depends on my cutoff radius even though I'm setting cuttoff radii well
above the size of the molecule. The gas phase simulations are 1 ns.
Does anyone know why this is or of a better way to do this?
Also, for systems as described, shouldn't the differences in enthalpy
correspond approximately to the changes in potential energy?
I'm somewhat concerned about having an overall charged system for the
solvated PME calculations, but if need by I can neutralize the systems.
Thank you in advance for any information.
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