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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.


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Next: Examples of input files Up: Alchemical Free Energy Methods1 Previous: Theoretical Background   Contents   Index
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