Hey guys,
Can someone please, explain what is the point of doing equilibration, for the proteins, in the "vacuum" in GROMACS? I know it is needed for the solution phase because one must equilibrate the solvent and ions around the protein. But what is the point of it in thevacuum and why do we do it in at a very low T?
Thanks!
Mary
When a protein is transferred from solution into vacuum, this process causes evaporation of the surrounding water. Upon evaporation, the proteins adjust their conformations to minimize the internal energy. Side-chains that previously were bonded to surrounding water molecules have to find new sites to interact with and thus a number of new intramolecular hydrogen bonds will be created. But this doesn’t change the entire conformation of the protein.
Besides some proteins were not soluble in cellular buffer systems . to study their interaction pattern, equilibration in vaccum can be performed.
Equilibration is the process whereby a many body system changes its internal structure from an arbitrary initial one under specified thermodynamic state conditions (Temperature,Pressure or volume,composition ,external fields etc) until its averaged properties do not change with time anymore (stationarity) although
fluctuations around a structure corresponding to a minimum of the free energy (Gibbs,Helmholtz) which has both an energy (enthalpy) and an entropy part occur.Therefore a protein structure transferred from solvent A to solvent B (i.e also no solvent) a5 specified requires equilibration to reach the region of phase space corresponding to the specified conditions and its the its sequence.
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