From d199f7449ab5b546633ff99e189a7d0c534dc4a7 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Fri, 6 Dec 2013 11:15:11 +0100
Subject: [PATCH] Improved doc for DISTANCE
---
src/colvar/Distance.cpp | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/src/colvar/Distance.cpp b/src/colvar/Distance.cpp
index 992ad73bf..2629aa540 100644
--- a/src/colvar/Distance.cpp
+++ b/src/colvar/Distance.cpp
@@ -33,6 +33,9 @@ namespace colvar{
//+PLUMEDOC COLVAR DISTANCE
/*
Calculate the distance between a pair of atoms.
+By default the distance is computed taking into account periodic
+boundary conditions. This behavior can be changed with the NOPBC flag.
+Moreover, single components (x,y, and z) can be also computed.
\par Examples
@@ -46,6 +49,37 @@ PRINT ARG=d1,d2,d2c.x
\endverbatim
(See also \ref PRINT).
+The following input computes the end-to-end distance for a polymer
+of 100 atoms and keeps it at a value around 5.
+\verbatim
+WHOLEMOLECULES ENTITY0=1-100
+e2e: DISTANCE ATOMS=1,100 NOPBC
+RESTRAINT ARG=e2e KAPPA=1 AT=5
+\endverbatim
+(See also \ref WHOLEMOLECULES and \ref RESTRAINT).
+
+Notice that NOPBC is used
+to be sure that if the end-to-end distance is larger than half the simulation
+box the distance is compute properly. Also notice that, since many MD
+codes break molecules across cell boundary, it might be necessary to
+use the \ref WHOLEMOLECULES keyword (also notice that it should be
+_before_ distance). The list of atoms provided to WHOLEMOLECULES
+here contains all the atoms between 1 and 100. Strictly speaking, this
+is not necessary. If you know for sure that atoms with difference in
+the index say equal to 10 are _not_ going to be farther than half cell
+you can e.g. use
+\verbatim
+WHOLEMOLECULES ENTITY0=1,10,20,30,40,50,60,70,80,90,100
+e2e: DISTANCE ATOMS=1,100 NOPBC
+RESTRAINT ARG=e2e KAPPA=1 AT=5
+\endverbatim
+Just be sure that the ordered list provide to WHOLEMOLECULES has the following
+properties:
+- Consecutive atoms should be closer than half-cell throughout the entire simulation.
+- Atoms required later for the distance (e.g. 1 and 100) should be included in the list
+
+
+
*/
//+ENDPLUMEDOC
--
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