[gmx-users] Mutation

susanta haldar susantahaldar at gmail.com
Tue Oct 7 12:00:26 CEST 2014

Hi all,

       I am doing mutation of some ligands in water and inside the protein
cavity as well and for that I chose a 3-step process to do that. 1st I do
discharging and then switching the vdw's between the ligands and then in
the 3rd step I do recharging again. For that I do need a four equilibrium
ensemble. In the discharging step in water, I do have the 1st ligand
equilibriated with charge and with non-charged and also the same for the
2nd ligand. Therefore whenever I have all those four equilibriated
ensembles, I do mutate between them with the softcore potential
(alpha=0.25, sigma=0.30).

   Now inside the protein cavity I also need the same four euilibriated
ensemble. I performed the equilibration but the non-charged ligands are
seems to me a bit unstable therefore I thought of taking only the state 0
and state 1 only  for the mutation inside the cavity. I neglected the

I got somehow reasonable results. Since we know the non-equilibrium CGI
should be started with the equilibrium ensemble therefore I am a bit
nervous to do that.

Could somebody direct me to do a better way or the strategy I am following,
if it is okay for the simulation of mutation.

thank you very much in advance.

Susanta Haldar
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic.

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