From 0448875a7ef58564be7e31a35ed25048da2bd378 Mon Sep 17 00:00:00 2001 From: Gareth Tribello <gareth.tribello@gmail.com> Date: Tue, 11 Sep 2018 16:43:40 +0100 Subject: [PATCH] Ran astyle --- src/colvar/Torsion.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/colvar/Torsion.cpp b/src/colvar/Torsion.cpp index 0c44d3f0f..0d1fed867 100644 --- a/src/colvar/Torsion.cpp +++ b/src/colvar/Torsion.cpp @@ -64,10 +64,10 @@ PRINT ARG=t1,t2 FILE=colvar STRIDE=10 Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein. Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the 4th residue of the protein. -Both of the previous examples specify that the torsion angle should be calculated based on the position of four atoms. +Both of the previous examples specify that the torsion angle should be calculated based on the position of four atoms. For the first example in particular the assumption when the torsion is specified in this way is that there are chemical -bonds between atoms 1 and 2, atoms 2 and 3 and atoms 3 and 4. In general, however, a torsional angle measures the angle -between two planes, which have at least one vector in common. As shown below, there is thus an alternate, more general, way +bonds between atoms 1 and 2, atoms 2 and 3 and atoms 3 and 4. In general, however, a torsional angle measures the angle +between two planes, which have at least one vector in common. As shown below, there is thus an alternate, more general, way through which we can define a torsional angle: \plumedfile @@ -75,8 +75,8 @@ t1: TORSION VECTOR1=1,2 AXIS=3,4 VECTOR2=5,6 PRINT ARG=t1 FILE=colvar STRIDE=20 \endplumedfile -This input instructs PLUMED to calculate the angle between the plane containing the vector connecting atoms 1 and 2 and the vector -connecting atoms 3 and 4 and the plane containing this second vector and the vector connecting atoms 5 and 6. We can even use +This input instructs PLUMED to calculate the angle between the plane containing the vector connecting atoms 1 and 2 and the vector +connecting atoms 3 and 4 and the plane containing this second vector and the vector connecting atoms 5 and 6. We can even use PLUMED to calculate the torsional angle between two bond vectors around the z-axis as shown below: \plumedfile -- GitLab