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Implementation of the free energy methods in NAMD

The procedures implemented in NAMD are particularly adapted for performing free energy calculations that split the $ \lambda $ reaction path into a number of non-physical, intermediate states, or ``windows''. Separate simulations can be started for each window. Alternatively, the TCL scripting ability of NAMD can be employed advantageously to perform the complete simulation in a single run. An example, making use of such a script, is supplied at the end of this section.

The following keywords can be used to run alchemical free energy calculations, whether FEP or TI. Each keyword has two variants: one that is used in FEP calculations and a second that should be used when performing TI. The FEP and TI variants are seperated by slashes like so: fepKeyword / tiKeyword, listing first the FEP keyword and second the TI keyword. The FEP and TI specific keywords should be used exclusively with FEP or TI, respectively, and should not be intermixed during a simulation.


next up previous contents index
Next: Examples of input files Up: Alchemical Free Energy Methods1 Previous: Theoretical Background   Contents   Index
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