[1] **viXra:1311.0073 [pdf]**
*submitted on 2013-11-11 11:03:19*

**Authors:** Asaf Farhi

**Comments:** 6 Pages.

Calculating free energy differences is a topic of substantial interest and has many applications including chemical
reactions which are used in organic chemistry, biochemistry and medicines. In equilibrium free energy methods that
are used in molecular simulations, one molecule is transformed into another to calculate the energy difference. However,
when the compared molecules have different number of atoms, these methods cannot be directly applied since the
corresponding transformation involves breaking covalent bonds which will cause a phase transition and impractical
sampling. Thus, Quantum Mechanical Simulations, which are significantly more demanding computationally, are usually
combined to calculate free energies of chemical reactions. Here we show that the free energies can be calculated
by simple classical molecular simulations followed by analytic or numerical calculations. In this method each molecule
is transformed into its replica with the VDW and Coulomb terms of the different atoms relaxed in order to eliminate
the partition function difference arising from these terms. Then, since each transformed system can be treated as
non interacting systems, the remaining difference in the (originally highly complex) partition function can be directly
calculated. Since molecular force fields can often be automatically generated and the calculations suggested here are
rather simple the method can form a basis for automated free energy computation of chemical reactions.

**Category:** Condensed Matter