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Corrections in analysis documentation

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This commit is contained in:
Tjerk Straatsma 1999-07-12 15:56:23 +00:00
parent d788765275
commit bfa6b7b55e
1 changed files with 12 additions and 4 deletions
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16
doc/user/analysis.tex
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@ -59,7 +59,8 @@ coordinates are read from a \nwchem\ restart file by the directive,
reference <string filename>
\end{verbatim}
where {\rm filename} is the name of an existing restart file.
where {\rm filename} is the name of an existing restart file. This
input is required.
\section{Selection}
@ -89,7 +90,8 @@ select 20 80 _N _CA _C
\section{File specification}
To specify the file to be analyzed
To specify the file to be analyzed when the analysis module is
invoked through a task directive
\begin{verbatim}
file [<integer firstfile> <integer lastfile>] <string filename>
@ -127,6 +129,9 @@ rmsdev
\section{Trajectory format conversion}
The command in this section only apply when the analysis module is
invoked though a task directive.
\par
To copy frames from specified files,
\begin{verbatim}
@ -173,13 +178,16 @@ from partial charges generated by the ESP module is generated
by the command
\begin{verbatim}
espgrid [ spacing <real spac default 0.05> ] \\
espgrid [ <integer chgset default 1> ] \\
[ spacing <real spac default 0.05> ] \\
[ range <real rcut default 0.3> ]
\end{verbatim}
The input is taken from the charges file generated by the ESP module. The
resulting plt formatted file can be graphically analyzed witht the
gOpenMol program.
gOpenMol program. The parameters chgset, spac and rcut specify the
charge set to be used, and the spacing and extent of the charge grid
evaluated.
The name of the charges file can be specified with