From 3e9e7cfe88149bb067634bb9e18fe8ef375c418d Mon Sep 17 00:00:00 2001
From: Tjerk Straatsma <straatsmatp@ornl.gov>
Date: Thu, 4 May 2000 21:27:06 +0000
Subject: [PATCH] Doc update

---
 doc/user/analysis.tex | 28 +++++++++++++++++++---------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/doc/user/analysis.tex b/doc/user/analysis.tex
index 9a91122056..c96f79ed17 100644
--- a/doc/user/analysis.tex
+++ b/doc/user/analysis.tex
@@ -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$^{-1}$.