| version 1.6 | version 1.7 |
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| {An output file named {\tt fepOutFile}.fep, generated by \NAMD, | {An output file named {\tt fepOutFile}.fep, generated by \NAMD, |
| contains the \FEP\ energies, dumped every {\tt fepOutFreq} steps.} | contains the \FEP\ energies, dumped every {\tt fepOutFreq} steps.} |
| | |
| | \item |
| | \NAMDCONFWDEF{fepVdWShiftCoeff}{\FEP\ radius-shifting coefficient} |
| | {positive decimal} |
| | {5.} |
| | {This is a radius-shifting coefficient of $\lambda$ that is used |
| | to construct the modified vdW interactions during alchemical FEP. Providing a positive value for {\tt fepVdWShiftCoeff} ensures that the vdW potential is finite everywhere for small values of $\lambda$, which significantly improves the accuracy and convergence of FEP calculations, and also prevents overlapping particles from making the simulation unstable. During FEP, the inter-atomic distances used in the Lennard-Jones potential are shifted |
| | according to: \\ |
| | $r^2 \rightarrow r^2 + {\rm fepVdWShiftCoeff} \times (1. - \lambda)$ |
| | } |
| | |
| | \item |
| | \NAMDCONFWDEF{fepVdwScaleExp}{\FEP\ Lennerd-Jones parameter scaling exponent} |
| | {decimal} |
| | {0.} |
| | {When constructing the modified vdW interactions during alchemical FEP, the Lennard-Jones parameters are scaled according to:\\ |
| | $A \rightarrow A \times \lambda^{2 \times {\rm fepVdwScaleExp}}$ \\ |
| | $B \rightarrow B \times \lambda^{\rm fepVdwScaleExp}$ |
| | } |
| | |
| | %\item |
| | %\NAMDCONFWDEF{fepElecLambdaDelay}{\FEP\ lambda ``delay" for electrostatics} |
| | %{positive decimal} |
| | %{0.} |
| | %{In order to avoid the FEP ``end-point catastrophe", it is often important to make sure that a growing particle does not have an unbounded potential right when it is created (in case that it appears on top of another particle). One way to deal with this for electrostatic interactions, is to allow a bounded scaled vdW potential (using a positive fepVdWShiftCoeff) to first repel all overlapping particles at low values of $\lambda$. As $\lambda$ increases, once the particles are repelled, it is now safe to turn on FEP electrostatics. fepElecLambdaDelay is the value of $\lambda$ at which electrostatic interactins are turned on and start ramping up linearly.} |
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| \end{itemize} | \end{itemize} |
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