Free energy calculations programs available

There is no unique, clearly defined protocol for free energy calculations. First of all, the available hardware imposes limitations, especially if very long simulations are required. Second, one is limited by the features and options of the computer software that is available. The molecular simulation programs that allow for free energy difference evaluations usually have specific options and features that reflect the programmers development of the methodology. Each program is likely to have features that are not found in any of the other codes. 

As suggested above, developments in AMBER tend to be problem-driven. Our conviction of the power and usefulness of free energy calculations, NMR refinement, and the importance of non-additive effects have made these distinctive features of the program. AMBER, like some of the other programs noted above, has always been available in source code form and that has encouraged others to use it as a platform for developments, often for our own and others benefit. 

A copy (5V4 inch floppy disk) of a menu-driven computer program to calculate Gibbs free energy of formation and change in Gibbs free energy for reactions (including random access data file of compound coefficients) is available for a nominal fee. For details, contact C. L. Yaws, Dept, of Chem. Eng. Lamar University, P.O. Box 10053, Beaumont, Texas 77710, USA. 

The calculation is based on the rule of thermodynamics, which states that a system will be in equilibrium when the Gibbs free energy is at a minimum. Cl The objective then is the minimization of the total free energy of the system and the calculation of equilibria at constant temperature and volume or at constant pressure. It is a complicated and lengthy calculation but, fortunately, several computer programs are now available that considerably simplify the task. PI... 

Thermodynamic reaction equilibrium for the naphthalene and tetralin hydrogenation to decalins was calculated according to Gibb s free energy change by the FLOWBAT program [12]. The results predict full conversion of both n hthalene and tetralin to decalins under the conditions studied. Moreover, thermodynamics favours the formation of trans-decalin, 93.5-96.6% in the temperature range 85-160°C [12]. The thermodynamic equilibrium of and A -octalin was not calculated since the required thermodynamic properties were not available. Weitkamp [7] has reported that the equilibrium ratio of the octalins varies from 15 to 3.5 at 0-200 C (5.9 and 3.6 at 100 and 177°C, respectively), with A -octalin the major component. 

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