[gmx-users] restraints

[Sadaf Rani]

Dear Gromacs users
I want to run free energy calculation of a protein-ligand complex by
putting distance, angle and dihedral restraints between ligand and protein.
Before that, I run 1ns MD (without free energy input) in order to know that
my ligand restraints are working well or otherwise. However, when I look at
the trajectory for these restraints, these values fluctuate during the
course of trajectory.  For example I kept distance between two atoms 4.08
but it ranges from 3.80 to 4.60 in trajectory. Similarly, dihedral angles
vary more than 10 degrees.
Is it right? should I go for free energy calculation? If not how should I
fix this?
I  need your suggestions, please.

Thanks

Sadaf