diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp index afcc74386dc12b508f8b48c4fd1e2b5370dffcb3..1d29a2f49ff92750fde4db33cf7be6523e57f2b8 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 11fd9123198a42f415e3e2f211b2b4d3ae38edf4..fc3a7f86e7d5e390949b664bedc077ae05a8a49c 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