From 02a73f6e1800b9a670fd31baddb2e7536fbe6fd7 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Sun, 13 May 2018 20:11:24 +0200
Subject: [PATCH] A few more verbatim -> plumedfile
---
src/multicolvar/VolumeBetweenContours.cpp | 4 ++--
src/pamm/PAMM.cpp | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp
index afcc74386..1d29a2f49 100644
--- a/src/multicolvar/VolumeBetweenContours.cpp
+++ b/src/multicolvar/VolumeBetweenContours.cpp
@@ -49,11 +49,11 @@ The input below calculates a density field from the positions of atoms 1-14400.
that are specified in the DENSITY action that are within a region where the density field is greater than
2.0 is then calculated.
-\verbatim
+\plumedfile
d1: DENSITY SPECIES=14401-74134:3 LOWMEM
fi: INENVELOPE DATA=d1 ATOMS=1-14400 CONTOUR={RATIONAL D_0=2.0 R_0=1.0} BANDWIDTH=0.1,0.1,0.1 LOWMEM
PRINT ARG=fi,rr.* FILE=colvar
-\endverbatim
+\endplumedfile
*/
//+ENDPLUMEDOC
diff --git a/src/pamm/PAMM.cpp b/src/pamm/PAMM.cpp
index 11fd91231..fc3a7f86e 100644
--- a/src/pamm/PAMM.cpp
+++ b/src/pamm/PAMM.cpp
@@ -59,13 +59,13 @@ looking through the example given below.
In this example I will explain in detail what the following input is computing:
-\verbatim
+\plumedfile
MOLINFO MOLTYPE=protein STRUCTURE=M1d.pdb
psi: TORSIONS ATOMS1=@psi-2 ATOMS2=@psi-3 ATOMS3=@psi-4
phi: TORSIONS ATOMS1=@phi-2 ATOMS2=@phi-3 ATOMS3=@phi-4
p: PAMM DATA=phi,psi CLUSTERS=clusters.dat MEAN1={COMPONENT=1} MEAN2={COMPONENT=2}
PRINT ARG=p.mean-1,mean-2 FILE=colvar
-\endverbatim
+\endplumedfile
The best place to start our explanation is to look at the contents of the clusters.dat file
--
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