From b0151b99196f9d1c916284b5f7e917963269618a Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Wed, 28 Jun 2017 07:30:42 +0200
Subject: [PATCH] Fixed typos in doc
(thanks to Pratyush Tiwary)
[makedoc]
---
src/colvar/ContactMap.cpp | 3 +++
src/function/FuncPathMSD.cpp | 6 +++---
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/src/colvar/ContactMap.cpp b/src/colvar/ContactMap.cpp
index f39a80bc0..57edf9e41 100644
--- a/src/colvar/ContactMap.cpp
+++ b/src/colvar/ContactMap.cpp
@@ -39,6 +39,9 @@ The transformed distance can be compared with a reference value in order to calc
between two contact maps. Each distance can also be weighted for a given value. CONTACTMAP can be used together
with \ref FUNCPATHMSD to define a path in the contactmap space.
+The individual contact map distances related to each contact can be accessed as components
+named `cm.contact-1`, `cm.contact-2`, etc, assuming that the label of the CONTACTMAP is `cm`.
+
\par Examples
The following example calculates switching functions based on the distances between atoms
diff --git a/src/function/FuncPathMSD.cpp b/src/function/FuncPathMSD.cpp
index 2020c0158..c2144d04b 100644
--- a/src/function/FuncPathMSD.cpp
+++ b/src/function/FuncPathMSD.cpp
@@ -65,7 +65,7 @@ ATOMS1=1,2 REFERENCE1=0.1
ATOMS2=3,4 REFERENCE2=0.5
ATOMS3=4,5 REFERENCE3=0.25
ATOMS4=5,6 REFERENCE4=0.0
-SWITCH=(RATIONAL R_0=1.5)
+SWITCH={RATIONAL R_0=1.5}
LABEL=c1
CMDIST
... CONTACTMAP
@@ -75,7 +75,7 @@ ATOMS1=1,2 REFERENCE1=0.3
ATOMS2=3,4 REFERENCE2=0.9
ATOMS3=4,5 REFERENCE3=0.45
ATOMS4=5,6 REFERENCE4=0.1
-SWITCH=(RATIONAL R_0=1.5)
+SWITCH={RATIONAL R_0=1.5}
LABEL=c2
CMDIST
... CONTACTMAP
@@ -85,7 +85,7 @@ ATOMS1=1,2 REFERENCE1=1.0
ATOMS2=3,4 REFERENCE2=1.0
ATOMS3=4,5 REFERENCE3=1.0
ATOMS4=5,6 REFERENCE4=1.0
-SWITCH=(RATIONAL R_0=1.5)
+SWITCH={RATIONAL R_0=1.5}
LABEL=c3
CMDIST
... CONTACTMAP
--
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