How to do Targeted MD

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

TMD

In NAMD, Targeted MD is very simple (Manual here):

TMD on
TMDk 200
TMDOutputFreq 1000
TMDFile target.pdb
TMDFirstStep 0
TMDLastStep 10000

There are a few precautions:

1. TMDk could range from 1 to 200, depending on your system. In general, smaller force means longer simulation and less distortion.
2. target.pdb can be smaller than the simulating system, i.e. you may remove water and ions. However, they should still be identical in the protein part, i.e. a truncated version but not arbitrary selections.
3. Think thoroughly how would you like to manipulate your system. Usually you can just blindly push the whole system towards your target.pdb by selecting all atoms (set occupancy to 1) with TMDk=200. Read this if you are ready to be an expert user of TMD.