Does the improper partial atom charge of the ligand have any effect on the MD simulation of the ligand protein complex? If so, will it will affect the calculation of potential mean force of the binding/unbinding event during steered molecular dynamics simulation?
Any error or inadequacy in parameters will have a negative impact on the outcome of the simulations. Depending on the magnitude of the error, the impact can be profound. Proper parametrization of any compound is of fundamental importance to any simulation.
Thank you justin for your reply. Out of curiosity I'm asking, will such a parameterization may lead to non-overlapping sampling windows during the calculation of PMF.
Probably not directly; overlap is more a function of force constant than anything else. The biggest problem is that all of the forces calculated in all of the windows will be wrong as a result of the incorrect parametrization. Overlap among badly calculated forces is useless.
Unfortunately, the description of electrostatics is both the most important and most difficult problem for such kind of tasks. That is what has to be paid special attention.
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