Editing Molecular dynamics (section)

== Incorporating solvent effects ==
In many simulations of a solute-solvent system the main focus is on the behavior of the solute with little interest of the solvent behavior particularly in those solvent molecules residing in regions far from the solute molecule.<ref>{{Cite book|title=Molecular Modelling: Principles and Applications| vauthors = Leach A |date=30 January 2001|publisher=Prentice Hall|isbn=9780582382107|edition= 2nd|location=Harlow|language=en|id={{ASIN|0582382106|country=uk}} }}</ref> Solvents may influence the dynamic behavior of solutes via random collisions and by imposing a frictional drag on the motion of the solute through the solvent. The use of non-rectangular periodic boundary conditions, stochastic boundaries and solvent shells can all help reduce the number of solvent molecules required and enable a larger proportion of the computing time to be spent instead on simulating the solute. It is also possible to incorporate the effects of a solvent without needing any explicit solvent molecules present. One example of this approach is to use a [[Potential of mean force|potential mean force]] (PMF) which describes how the free energy changes as a particular coordinate is varied. The free energy change described by PMF contains the averaged effects of the solvent.

Without incorporating the effects of solvent simulations of macromolecules (such as proteins) may yield unrealistic behavior and even small molecules may adopt more compact conformations due to favourable van der Waals forces and electrostatic interactions which would be dampened in the presence of a solvent.<ref>{{Cite book | vauthors = Leach AR |url=https://www.worldcat.org/oclc/45008511 |title=Molecular modelling : principles and applications |date=2001 |publisher=Prentice Hall |isbn=0-582-38210-6 |edition=2nd |location=Harlow, England |pages=320 |oclc=45008511}}</ref>