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Im performing MD simulation of Insulin protein with Choline-Geranate ionic liquid by preparing different system of different mole fraction.
the system was prepared using “gmx insert-molecules” and the number of solvent was restricted by using “-maxsol”.
I perform NVT followed by NPT equilibrium for 10ns.
this is the snapshot of MD.gro output .
(the box size was reduced after NPT and MD run)
My question is that “am I following right procedure or wrong?”
please suggest me, “if I following wrong procedure then guide me what procedure should I follow?”
First prepare a solvent only box (using gmx insert-molecules or Packmol), run minimisation and equilibration steps and then a production run. The duration of production run can be anything from 5 ns to longer depending on your solvent characteristics. I have found that water and small organic molecules typically require 2-5 ns.
Use the equilibrated solvent box with gmx solvate.
