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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. However, the setup of sequential alchemical trsnaformations can be simplified by calling the script library fep.tcl, found in the lib/alch directory of the NAMD distribution. This library provides two helper procedures, runFEP to run a series of evenly spaced windows, and runFEPlist to specify a list of $ \lambda $ values to be sampled.

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
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