[gmx-users] Free Energy Question

Fabian Casteblanco fabian.casteblanco at gmail.com
Mon Oct 3 21:28:08 CEST 2011

Hello all,

I have a general question about calculating free energies.  I recently
used g_bar to calculate the free energies of decoupling coulombic and
vdW forces of a solute molecule in solvent.  I now need to calculate
the free energy of a solute molecule mutating to a new molecule
(identical but with an extra -CH3 group) in a vacuum and in a solvent.
 Does anybody know if it would be better to use g_Bar again but this
time having the extra -CH3 group completely decoupled by itself or
with it be better to use the older slow-growth method that the Gromacs
Manual talks about in Sec 3.12.  I'm not sure if there is a way to
only decouple a certain part of a molecule using the g_bar method,
rather than decoupling the entire molecule.

Thanks for your help.

Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com

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