How to do enhanced sampling

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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
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