[gmx-users] Preparing dual topology for free energy calculation

[Tushar Ranjan Moharana]

Hi everyone,
I want to calculate difference in folding free energy due to certain
mutations. I want to follow the slow growth method as mentioned in:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html
However I don't know how to prepare dual topology (even after reading
manual, section  5.7.4). I want to use gromos 53a6 force field. Can anyone
tell me how to prepare dual topology. Any link to read or tutorial will be
of great help.

Thanks a lot for the help.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB