How to do enhanced sampling

Essential Dynamics Sampling

1. Merge start and end structure in one trajectory
2. gmx covar -f merged.trr -s start.pdb
3. gmx make_edi -f eigenvec.trr -s ionized.pdb -n index.ndx -radcon 1 -tar end.pdb
4. gmx mdrun -ei sam.edi -deffnm ed