version 1.32 | version 1.33 |
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For an exnihilated particle, vdW interactions are fully decoupled at $\lambda$=0. The coupling of vdW interactions to the simulation is then increased with increasing values of $\lambda$ such that at values of $\lambda$ greater than or equal to {\tt alchVdwLambdaEnd} the vdW interactions of the exnihilated particle are fully coupled to the simulation. | For an exnihilated particle, vdW interactions are fully decoupled at $\lambda$=0. The coupling of vdW interactions to the simulation is then increased with increasing values of $\lambda$ such that at values of $\lambda$ greater than or equal to {\tt alchVdwLambdaEnd} the vdW interactions of the exnihilated particle are fully coupled to the simulation. |
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For an annihilated particle, vdW interactions are completely coupled to the simulation for $\lambda$ values between 0 and (1 - {\tt alchVdwLambdaEnd}). Then, vdW interactions of the annihilated particle are linearly decoupled over the range of $\lambda$ values between (1 - {\tt alchVdwLambdaEnd}) and 1.0. VdW interactions are only fully decoupled when $\lambda$ reaches 1.0. | For an annihilated particle, vdW interactions are completely coupled to the simulation for $\lambda$ values between 0 and (1 - {\tt alchVdwLambdaEnd}). Then, vdW interactions of the annihilated particle are linearly decoupled over the range of $\lambda$ values between (1 - {\tt alchVdwLambdaEnd}) and 1.0. VdW interactions are only fully decoupled when $\lambda$ reaches 1.0. |
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| {\bf New as of version 2.12:} The energy and virial terms added by |
| {\tt LJcorrection on} are now also controlled by the vdW $\lambda$ schedule. |
| The average Lennard-Jones $A$ and $B$ 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 \emph{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. |
| } |
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| \item |
| \NAMDCONFWDEF {alchBondLambdaEnd}{Value of $\lambda$ to cancel bonded interactions} |
| {positive decimal} |
| {1.0} |
| {{\bf New as of version 2.12} Bonded terms involving alchmical atoms |
| are now also scaled on a schedule similar to vdW interactions. {\bf In some |
| cases this will produce different behavior from the old defaults.} In order to |
| regain the old behavior (potentially theoretically unsound!), simply set |
| {\tt alchBondLambdaEnd} to 0. See also {\tt alchBondDecouple}. |
| } |
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| \item |
| \NAMDCONFWDEF {alchBondDecouple}{Enable scaling of bonded terms within alchemical groups} |
| {{\tt on} or {\tt off}} |
| {{\tt off}} |
| {If {\tt alchBondDecouple} is {\tt on} (not the default!), then bonded terms |
| between alchemical atoms \emph{in the same group} are also scaled. This means |
| that alchemical atoms are annihilated into ideal gas atoms instead of ideal gas |
| molecules. In this case it is recommended to use the approach of Axelsen and |
| Li~\cite{Axelsen1998} by way of the {\tt extraBonds} keyword. Using |
| {\tt alchBondDecouple} {\tt on} is strictly necessary if it is desired to have |
| the endpoint energies of a dual-topology PSF match those of a non-alchemical |
| PSF. |
| } |
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\item | \item |