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Subsections

New Commands and Keywords

The constant-pH implementation is largely implemented in Tcl and can be found in /lib/namdcph/namdcph.tcl, where the base directory is the NAMD source home directory. When that file has been loaded with a suitable source command, the following commands and keywords are available and appear to the user in a way similar to NAMD syntax. The most significant change from normal NAMD usage is that there is generally no need to use the run command. One should instead use the new cphRun command; this can only be used once per script for now. NB, all commands and keywords are currently case sensitive!

cphRun $ <$ Run constant-pH MD $ >$
Arguments: $ <$ numsteps$ >$ $ [$ numcycles$ ]$
Defaults: numcycles = 1
Description: Execute numcycles cycles of constant-pH MD with the current settings. Each cycle consists of 1) a neMD/MC move in both configuration and protonation space and 2) MD based sampling in configuration space. By default, configuration space sampling simply consists of numsteps dynamics, as in conventional MD. The nature of the neMD/MC moves, however, is more elaborate and controlled by other keywords, many of which are required (see below).

Required Keywords

Commonly Used Options

Specialized Options

\fbox{
\begin{minipage}[ht!]{15.3cm}
\addtolength{\baselineskip}{0.225\baselin...
...gorous of testing and may be prone
to unintended consequences.
\end{minipage}}


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Next: Minimal Examples Up: Constant-pH Simulations 1 Previous: Implementation Details   Contents   Index
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