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Tjerk Straatsma 2000-05-04 21:27:06 +00:00
parent 7784c0c0df
commit 3e9e7cfe88
1 changed files with 19 additions and 9 deletions
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doc/user/analysis.tex
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@ -146,19 +146,19 @@ rmsd
To define a bond:
\begin{verbatim}
bond <integer ibonc> <string atomi> <string atomj>
bond <integer ibond> <string atomi> <string atomj>
\end{verbatim}
To define an angle:
\begin{verbatim}
angle <integer ibonc> <string atomi> <string atomj> <string atomk>
angle <integer iangle> <string atomi> <string atomj> <string atomk>
\end{verbatim}
To define a torsion:
\begin{verbatim}
torsion <integer ibonc> <string atomi> <string atomj> \
torsion <integer itorsion> <string atomi> <string atomj> \
<string atomk> <string atoml>
\end{verbatim}
@ -171,6 +171,12 @@ The atom string in these definitions takes the form
for solute and solvent atom specification, respectively.
To define charge distribution in z-direction:
\begin{verbatim}
charge_distribution <integer bins>
\end{verbatim}
To perform the coordinate analysis:
\begin{verbatim}
@ -256,7 +262,7 @@ in the \ecce\ trajectory viewer can be specified with
label 1 mistyrose 34 45
\end{verbatim}
\section{Electrostatic potential from partial charges}
\section{Electrostatic potentials}
A file in plt format of the electrostatic potential resulting
from partial charges generated by the ESP module is generated
@ -264,16 +270,20 @@ by the command
\begin{verbatim}
esp <string xfile> [ <integer spacing default 10> ] \
[ <real rcut 0.3> ] [periodic [<integer iper>]] \
[ <real rcut default 1.0> ] [periodic [<integer iper default 3>]] \
[ <string pltfile> ]
\end{verbatim}
The input coordinates are taken from the {\rm xyzq} file that can
be genersted from a {\rm rst} by the prepare module. Parameters
spacing and rcut specify the spacing and extent of the charge grid
evaluated. Periodic boundaries will be used if \verb+periodic+
be genersted from a {\rm rst} by the prepare module. Parameter
spacing specifies the number of gridpoints per nm, rcut specifies
extent of the charge grid beyond the molecule.
Periodic boundaries will be used if \verb+periodic+
is specified. If \verb+iper+ is set to 2, periodic boundary
conditions are applied in x and y dimensions only.
conditions are applied in x and y dimensions only. If \verb+periodic+
is specified, a negative value of \verb+rcut+ will extend the grid
in the periodic dimensions by abs(\verb+rcut+), otherwise this value
will be ignored in the periodic dimensions.
The resulting {\rm plt} formatted file pltfile can be
viewed with the gOpenMol program. The resulting electrostatic
potential grid is in units of kJ\ mol$^{-1}$e$^{-1}$.