On 03/25/2010 07:11 AM, abdullah ahmed wrote:
I have a question related to the calculation of energy during optimization. What are the units (Joules/calories/ Kilo joules etc?) of the energy calculated? (The "current energy" value in the log-file, for example, is a number. I'd like to know the units that correspond to it)
The energy doesn't have any units - it is simply the negative log of the molecular probability density function. However, since the CHARMM forcefield is added in, the terms are scaled by RT so they are roughly comparable to CHARMM. Thus, the units are nominally kcal/mol.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage