[gmx-users] free energy calculation

[Tony Zhou]

Dear All,

I am a quite new user for Gromacs so I really appreciate your helps.

I am dealing with the free energy calculation for two enantiomers. For that
I need to change H(connected to CA) to CH3 for one molecule and other way
around for another molecule, but such H is not included in the topology file
of Gromacs.  Just wonder how to define/add it in the library. Is there any
standard protocol to set up the free engergy calculation in GROMACS? The
description in Gromacs mannual is not so clear to me even I checked the many
discussions in the mailing list.

Regards,

Tony,