Alchemical free energy calculations

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
While performing the alchemical free energy calculations for protein ligand binding :
The topology file for the protein ligand complex system have a section called intermolecular interactions , which explains distance , angle and dihedral restraints .

Can someone please explain the meaning of

bA kA bB kB

thA fcA thB fcB

2

Reference bond lengths and associated force constants in the A- and B-states, respectively

Same thing, but for angles.

3

Thanks

How do we assing the force constant for A and B state . How is it calculated ?