From 681b8ea0e63a2827df746431d176e35e9150f07d Mon Sep 17 00:00:00 2001 From: Carlo Camilloni <carlo.camilloni@gmail.com> Date: Sun, 16 Oct 2016 18:28:03 +0200 Subject: [PATCH] more docs on CS2Backbone [makedoc] --- src/colvar/CS2Backbone.cpp | 4 ++++ user-doc/tutorials/belfast-9a.txt | 4 +++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/src/colvar/CS2Backbone.cpp b/src/colvar/CS2Backbone.cpp index 9c433ef2a..97d50f275 100644 --- a/src/colvar/CS2Backbone.cpp +++ b/src/colvar/CS2Backbone.cpp @@ -63,6 +63,10 @@ shift as in \cite Camilloni:2012je \cite Camilloni:2013hs (see \ref STATS and CamShift calculation is relatively heavy because it often uses a large number of atoms, in order to make it faster it is currently parallelised with \ref OpenMP. +As a general rule, when using \ref CS2BACKBONE or other experimental restraints it is better to +increase the accuracy of the constraint algorithm due to the increased strain on the bonded structure. +In the case of GROMACS it is safer to use lincs-iter=2 and lincs-order=6. + In general the system for which chemical shifts are calculated must be completly included in ATOMS and a TEMPLATE pdb file for the same atoms should be provided as well in the folder DATA. The atoms are made automatically whole unless NOPBC is used, in particular if the system is made of diff --git a/user-doc/tutorials/belfast-9a.txt b/user-doc/tutorials/belfast-9a.txt index 1b8ea8560..7283914dd 100644 --- a/user-doc/tutorials/belfast-9a.txt +++ b/user-doc/tutorials/belfast-9a.txt @@ -33,7 +33,9 @@ and Residual Dipolar couplings/pseudocontact shifts \ref RDC. In the following we will write the \ref CS2BACKBONE collective variable similar to the one used in Granata et al. (2013) (while the collective variable is still proportional to the square sum of the deviation of the calculated and experimental chemical shifts divided by a typical error, the exact definition is not the same. The sum is not done anymore with a flat bottom difference and the error used are not the one -published, so the exact result of the scoring function can be different). +published, so the exact result of the scoring function can be different). + +As a general rule, when using \ref CS2BACKBONE or other experimental restraints it is better to increase the accuracy of the constraint algorithm due to the increased strain on the bonded structure. In the case of GROMACS it is safer to use lincs-iter=2 and lincs-order=6. \verbatim prot: GROUP ATOMS=1-862 -- GitLab