[gmx-users] Finding free energy differences between conformation clusters on plumed

[Billy Williams-Noonan]

 Hi All,


   - I ran a well-tempered metadynamics simulation usinf plumed on a cyclic
   peptide [say cyclo(ABCDEF) ].
   - I biased it in terms of three internal distances, d7, d8 and d9, where
   d7 B->E, d8 was A->D and d9 was C->F from the example above.
   - This simulation ran to convergence until the Gaussian height reached
   zero and the metadynamics bias did not change, and neither did the FES for
   40ns.  The simulation ran for 100ns all up.
   - I have an FES for d7, d8 and d9.
   - I have clustred all conformers across the entire metadynamics
   simulation into 6 distinct groups.  This clustering was based on the
   c-alpha coordinates and how they varied across the metaD simulation.
   - I found that cluster 6 was the lowest energy conformation based on
   measurements of d7, d8 and d9 in those clusters, in conjunction with the
   FES of d7, d8 and d9.

My question is, could I run 6 simulations using pull-code constraints on
Gromacs on d7, d8 and d9, to lock the conformation into one of the 6
clusters for every simulation, and then use *gmx energy *to print the
energy of the constraints for each simulation?  That way I would be able to
find the energy required to keep the peptide in a certain conformation.
The lower the energy required, the lower the energy state of that
conformer.  Would I be able to find relative free energies between the
conformers in this way?

Best regards,

Billy

-- 
Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon

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