[gmx-users] Pulling

[mohsen ramezanpour]

Dear All
Afew question about Pulling in Umberella Sampling

1-the goal of pulling is making some primary structures (in different
distances) to do umberella sampling for each one of them.
 I can make these states by transporting my ligands along a vector to
prepare these primary structures.Is this correct?Now I can do US for each
one!without any need to doing pulling.

2-Why do we keep fix the relative orientation of Protein-ligand during the
pulling ? I think changing the orientation of ligand during the
pulling(suppose the protein is restrain) can chang our result?
  Because our umbrella sampling maintain this orientation too.am I right?

Thanks in advance
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