| version 1.33 | version 1.34 |
|---|
| |
| \item | \item |
| \NAMDCONFWDEF {alchBondLambdaEnd}{Value of $\lambda$ to cancel bonded interactions} | \NAMDCONFWDEF {alchBondLambdaEnd}{Value of $\lambda$ to cancel bonded interactions} |
| {positive decimal} | {positive decimal} |
| {1.0} | {0.0} |
| {{\bf New as of version 2.12} Bonded terms involving alchmical atoms | {{\bf New as of version 2.12} Bonded terms involving alchemical atoms may now |
| are now also scaled on a schedule similar to vdW interactions. {\bf In some | also be scaled on a schedule similar to vdW interactions. Although this is more |
| cases this will produce different behavior from the old defaults.} In order to | theoretically sound in many situations, this behavior is off by default. |
| regain the old behavior (potentially theoretically unsound!), simply set | |
| {\tt alchBondLambdaEnd} to 0. See also {\tt alchBondDecouple}. | |
| } | } |
| | |
| \item | \item |
| \NAMDCONFWDEF {alchBondDecouple}{Enable scaling of bonded terms within alchemical groups} | \NAMDCONFWDEF {alchBondDecouple}{Enable scaling of bonded terms within alchemical groups} |
| {{\tt on} or {\tt off}} | {{\tt on} or {\tt off}} |
| {{\tt off}} | {{\tt off}} |
| {If {\tt alchBondDecouple} is {\tt on} (not the default!), then bonded terms | {This is essentially a bonded term analogue of the {\tt alchDecouple} keyword. |
| between alchemical atoms \emph{in the same group} are also scaled. This means | Setting {\tt alchBondDecouple on}, causes bonded terms between alchemical |
| that alchemical atoms are annihilated into ideal gas atoms instead of ideal gas | atoms \emph{in the same group} to also be scaled. This means that alchemical |
| molecules. In this case it is recommended to use the approach of Axelsen and | 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 | Li~\cite{Axelsen1998} by way of the {\tt extraBonds} keyword. Using |
| {\tt alchBondDecouple} {\tt on} is strictly necessary if it is desired to have | {\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 | the endpoint (potential) energies of a dual-topology PSF match those of a |
| PSF. | non-alchemical PSF. |
| } | } |
| | |
| | |
| |
| | |
| \subsubsection{Thermodynamic Integration } | \subsubsection{Thermodynamic Integration } |
| | |
| | When running TI free energy calculations, the {\tt elec\_dU/dl}, |
| When running TI free energy calculations, the {\tt elec\_dU/dl} and {\tt | {\tt vdW\_dU/dl}, and {\tt bond\_dU/dl} values reported in {\tt alchOutFile} |
| vdW\_dU/dl} values reported in {\tt tiOutFile} are the derivatives of the | are the derivatives of the internal energy with respect to the scaling factors |
| internal energy with respect to $\lambda$ --- \ie~$\frac{\partial | for each interaction type (\ie~electrostatics, etc.). {\tt dU/dl} values are |
| U}{\partial\lambda}$ for electrostatics and, van der Waals, respectively. {\tt | locally averaged over the last {\tt alchOutFreq} steps. Cumulative |
| dU/dl} values are averages over the last {\tt tiOutFreq} steps. Cumulative | |
| averages for each component are reported alongside in the {\tt \_avg} columns. | averages for each component are reported alongside in the {\tt \_avg} columns. |
| | |
| | The electrostatic, vdW, and bond values are separated following a partition |
| The electrostatics and vdW are separated following a partition scheme --- that | scheme --- that is, the ``appearing'' and the ``disappearing'' atoms are |
| is, the ``appearing'' and the ``disappearing'' atoms are accounted for | accounted for separately. ``Partition 1'' contains those atoms whose |
| separately. ``Partition 1'' contains those atoms whose interactions are | interactions are switched up as $\lambda$ increases --- \ie~flagged with |
| switched up as $\lambda$ increases --- \ie~flagged with {\tt 1} in the {\tt | {\tt 1} in the {\tt alchFile}. ``Partition 2'' represents those atoms whose |
| alchFile}. ``Partition 2'' represents those atoms whose interactions are | interactions are switched down as $\lambda$ increases --- \ie~flagged with |
| switched down as $\lambda$ increases --- \ie~flagged with {\tt -1}. $\Delta A$ | {\tt -1}. $\Delta A$ values for each component are obtained by integrating from |
| values for each component are obtained by integrating from $\lambda=0$ to $1$ | $\lambda=0$ to $1$ using the respective {\tt ELEC / VDW / BOND LAMBDA} listed |
| using the respective {\tt ELEC / VDW LAMBDA} listed for each partition after | for each partition after the title. |
| the title. | |
| | {\bf New as of version 2.12:} The output in {\tt alchOutFile} has been |
| | extensively revised and now more closely matches the NAMD standard output. |
| Analysis is handled by the {\tt NAMD\_ti} script, available from | Additional accounting for bonded term scaling is now also included. |
| \begin{quote} | |
| http://www.ks.uiuc.edu/Research/namd/utilities/ | %% Analysis is handled by the {\tt NAMD\_ti} script, available from |
| \end{quote} | %% \begin{quote} |
| | %% http://www.ks.uiuc.edu/Research/namd/utilities/ |
| | %% \end{quote} |
| Although the output format of {\tt NAMD\_ti.pl } may appear to lend itself easily to interpretation of the | |
| individual contributions to the free energy total (elec and vdW for each partition), this is rarely | |
| appropriate as these values are path-dependent. For example, an output such as | %% Although the output format of {\tt NAMD\_ti.pl } may appear to lend itself easily to interpretation of the |
| | %% individual contributions to the free energy total (elec and vdW for each partition), this is rarely |
| | %% appropriate as these values are path-dependent. For example, an output such as |
| \begin{verbatim} | |
| |-----------------------------------------------| | |
| | | elec | vdW | Subtotal | | %%\begin{verbatim} |
| |-----------------------------------------------| | %% |-----------------------------------------------| |
| | Part. 1 | -0.5748 | -6.3452 | -6.9200 | | %% | | elec | vdW | Subtotal | |
| | Part. 2 | 0.5391 | 4.9387 | 5.4778 | | %% |-----------------------------------------------| |
| |-----------------------------------------------| | %% | Part. 1 | -0.5748 | -6.3452 | -6.9200 | |
| | Subtotal| 0.6048 | 0.3293 | -12.3978 | | %% | Part. 2 | 0.5391 | 4.9387 | 5.4778 | |
| |-----------------------------------------------| | %% |-----------------------------------------------| |
| Total deltaG for transition lambda 0 -> 1: -12.3978 | %% | Subtotal| 0.6048 | 0.3293 | -12.3978 | |
| \end{verbatim} | %% |-----------------------------------------------| |
| | %% Total deltaG for transition lambda 0 -> 1: -12.3978 |
| | %%\end{verbatim} |
| \noindent may encourage interpretations along the lines of "the free energy for | |
| switching on the van der Waals interactions for the atoms of partition 1 was | |
| -6.35kcal/mol". This is only correct in the very narrow context of the | %%\noindent may encourage interpretations along the lines of "the free energy for |
| simulation setup and parameters used in this case and is not informative in a | %%switching on the van der Waals interactions for the atoms of partition 1 was |
| broader sense. | %%-6.35kcal/mol". This is only correct in the very narrow context of the |
| | %%simulation setup and parameters used in this case and is not informative in a |
| | %%broader sense. |
| | |
| | |
| %\begin{figure}[ht] | %\begin{figure}[ht] |