The procedures implemented in NAMD are particularly adapted for performing free energy calculations that split the 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 values to be sampled.
The following keywords can be used to run alchemical free energy calculations, whether FEP or TI.
In the current implementation, the electrostatic interactions of an exnihilated, or appearing, particle are linearly coupled to the simulation over the value range of alchElecLambdaStart - 1.0. At values less than or equal to the user-defined value of alchElecLambdaStart, electrostatic interactions of the exnihilated particle are fully decoupled from the simulation. Coupling of electrostatic interactions then increases linearly for increasing values of until =1.0, at which point electrostatic interactions of the exnihilated particle are fully coupled to the simulation.
For annihilated, or vanishing, particles the electrostatic interactions are linearly decoupled from the simulation over the value range of 0 - (1.0 - alchElecLambdaStart). At =0 electrostatic interactions are fully coupled to the simulation, and then linearly decreased with increasing such that at values greater than or equal to (1.0 - alchElecLambdaStart) electrostatic interactions are completely decoupled from the simulation. Two examples, shown in Figure 7, describe the relationship between the user-defined value of and the coupling of electrostatic or vdW interactions to the simulation.
For an exnihilated particle, vdW interactions are fully decoupled at =0. The coupling of vdW interactions to the simulation is then increased with increasing values of such that at values of greater than or equal to alchVdwLambdaEnd the vdW interactions of the exnihilated particle are fully coupled to the simulation.
For an annihilated particle, vdW interactions are completely coupled to the simulation for values between 0 and (1 - alchVdwLambdaEnd). Then, vdW interactions of the annihilated particle are linearly decoupled over the range of values between (1 - alchVdwLambdaEnd) and 1.0. VdW interactions are only fully decoupled when reaches 1.0.
New as of version 2.12: The energy and virial terms added by LJcorrection on or LJcorrectionAlt on are now also controlled by the vdW schedule. The average Lennard-Jones and coefficients are computed separately at both endpoints and then coupled linearly. In most practical situations the energy difference is extremely negligible, but this is more theoretically sound than the old behavior of averaging both endpoints together. However, the kinetic energy component of the virial does still count the endpoints together, as if annihilated alchemical atoms were an ideal gas. Again, this is likely quite negligible, nor is it clear that this should be treated specially.