From 188429af06f4dd12725d5bdf7906d458beba9170 Mon Sep 17 00:00:00 2001 From: Thomas Ullmann Date: Thu, 7 Feb 2019 18:14:38 +0100 Subject: [PATCH] separated .rst documentation of dihedral PCA and hydrogen-bonds The section of the reference manual on hydrogen-bonds was included in dihedral-pca.rst. This hindered insertion of a section on an analysis method related to PCA right after the dihedral PCA section. Change-Id: I4d7c88624a12fc516cb63465098060fc871cc987 --- docs/CMakeLists.txt | 1 + docs/reference-manual/analysis.rst | 1 + docs/reference-manual/analysis/dihedral-pca.rst | 144 ++++----------------- .../{dihedral-pca.rst => hydrogen-bonds.rst} | 30 ----- 4 files changed, 30 insertions(+), 146 deletions(-) rewrite docs/reference-manual/analysis/dihedral-pca.rst (68%) copy docs/reference-manual/analysis/{dihedral-pca.rst => hydrogen-bonds.rst} (68%) diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt index 55a43089e8..8ad2e04f5a 100644 --- a/docs/CMakeLists.txt +++ b/docs/CMakeLists.txt @@ -245,6 +245,7 @@ if (SPHINX_FOUND) reference-manual/analysis/rmsd.rst reference-manual/analysis/covariance-analysis.rst reference-manual/analysis/dihedral-pca.rst + reference-manual/analysis/hydrogen-bonds.rst reference-manual/analysis/protein-related.rst reference-manual/analysis/interface-related.rst) # The image files have also been ordered by the respective diff --git a/docs/reference-manual/analysis.rst b/docs/reference-manual/analysis.rst index 4c698f9bdc..d789d3d40d 100644 --- a/docs/reference-manual/analysis.rst +++ b/docs/reference-manual/analysis.rst @@ -30,6 +30,7 @@ different analysis tools are presented. analysis/rmsd analysis/covariance-analysis analysis/dihedral-pca + analysis/hydrogen-bonds analysis/protein-related analysis/interface-related diff --git a/docs/reference-manual/analysis/dihedral-pca.rst b/docs/reference-manual/analysis/dihedral-pca.rst dissimilarity index 68% index 8c31695026..a49b684dff 100644 --- a/docs/reference-manual/analysis/dihedral-pca.rst +++ b/docs/reference-manual/analysis/dihedral-pca.rst @@ -1,116 +1,28 @@ -Dihedral principal component analysis -------------------------------------- - -| :ref:`gmx angle `, :ref:`gmx covar `, - :ref:`gmx anaeig ` -| Principal component analysis can be performed in dihedral - space \ :ref:`172 ` using |Gromacs|. You start by defining the - dihedral angles of interest in an index file, either using - :ref:`gmx mk_angndx ` or otherwise. Then you use the - :ref:`gmx angle ` program with the ``-or`` flag to - produce a new :ref:`trr` file containing the cosine and sine - of each dihedral angle in two coordinates, respectively. That is, in - the :ref:`trr` file you will have a series of numbers - corresponding to: cos(\ :math:`\phi_1`), sin(\ :math:`\phi_1`), - cos(\ :math:`\phi_2`), sin(\ :math:`\phi_2`), ..., - cos(\ :math:`\phi_n`), sin(\ :math:`\phi_n`), and the array is padded - with zeros, if necessary. Then you can use this :ref:`trr` - file as input for the :ref:`gmx covar ` program and perform - principal component analysis as usual. For this to work you will need - to generate a reference file (:ref:`tpr`, - :ref:`gro`, :ref:`pdb` etc.) containing the same - number of “atoms” as the new :ref:`trr` file, that is for - :math:`n` dihedrals you need 2\ :math:`n`/3 atoms (rounded up if not - an integer number). You should use the ``-nofit`` option - for :ref:`gmx covar ` since the coordinates in the dummy - reference file do not correspond in any way to the information in the - :ref:`trr` file. Analysis of the results is done using - :ref:`gmx anaeig `. - -Hydrogen bonds --------------- - -| :ref:`gmx hbond ` -| The program :ref:`gmx hbond ` - analyzes the *hydrogen bonds* (H-bonds) between all possible donors D - and acceptors A. To determine if an H-bond exists, a geometrical - criterion is used, see also :numref:`Fig. %s `: - - .. math:: \begin{array}{rclcl} - r & \leq & r_{HB} & = & 0.35~\mbox{nm} \\ - \alpha & \leq & \alpha_{HB} & = & 30^o \\ - \end{array} - :label: eqnhbondgeomtric - -.. _fig-hbond: - -.. figure:: plots/hbond.* - :width: 7.50000cm - - Geometrical Hydrogen bond criterion. - -The value of :math:`r_{HB} = 0.35 \mathrm{nm}` corresponds to the first minimum -of the RDF of SPC water (see also :numref:`Fig. %s `). - -The program :ref:`gmx hbond ` analyzes all hydrogen bonds -existing between two groups of atoms (which must be either identical or -non-overlapping) or in specified donor-hydrogen-acceptor triplets, in -the following ways: - -.. _fig-hbondinsert: - -.. figure:: plots/hbond-insert.* - :width: 7.50000cm - - Insertion of water into an H-bond. (1) Normal H-bond between two - residues. (2) H-bonding bridge via a water molecule. - -- Donor-Acceptor distance (:math:`r`) distribution of all H-bonds - -- Hydrogen-Donor-Acceptor angle (:math:`\alpha`) distribution of all - H-bonds - -- The total number of H-bonds in each time frame - -- The number of H-bonds in time between residues, divided into groups - :math:`n`-:math:`n`\ +\ :math:`i` where :math:`n` and - :math:`n`\ +\ :math:`i` stand for residue numbers and :math:`i` goes - from 0 to 6. The group for :math:`i=6` also includes all H-bonds for - :math:`i>6`. These groups include the - :math:`n`-:math:`n`\ +\ :math:`3`, :math:`n`-:math:`n`\ +\ :math:`4` - and :math:`n`-:math:`n`\ +\ :math:`5` H-bonds, which provide a - measure for the formation of :math:`\alpha`-helices or - :math:`\beta`-turns or strands. - -- The lifetime of the H-bonds is calculated from the average over all - autocorrelation functions of the existence functions (either 0 or 1) - of all H-bonds: - - .. math:: C(\tau) ~=~ \langle s_i(t)~s_i (t + \tau) \rangle - :label: eqnhbcorr - -- with :math:`s_i(t) = \{0,1\}` for H-bond :math:`i` at time - :math:`t`. The integral of :math:`C(\tau)` gives a rough estimate of - the average H-bond lifetime :math:`\tau_{HB}`: - - .. math:: \tau_{HB} ~=~ \int_{0}^{\infty} C(\tau) d\tau - :label: eqnhblife - -- Both the integral and the complete autocorrelation function - :math:`C(\tau)` will be output, so that more sophisticated analysis - (*e.g.* using multi-exponential fits) can be used to get better - estimates for :math:`\tau_{HB}`. A more complete analysis is given in - ref. \ :ref:`173 `; one of the more fancy option is the Luzar - and Chandler analysis of hydrogen bond kinetics \ :ref:`174 `, :ref:`175 `. - -- An H-bond existence map can be generated of dimensions - *# H-bonds*\ :math:`\times`\ *# frames*. The ordering is identical to - the index file (see below), but reversed, meaning that the last - triplet in the index file corresponds to the first row of the - existence map. - -- Index groups are output containing the analyzed groups, all - donor-hydrogen atom pairs and acceptor atoms in these groups, - donor-hydrogen-acceptor triplets involved in hydrogen bonds between - the analyzed groups and all solvent atoms involved in insertion. - +Dihedral principal component analysis +------------------------------------- + +| :ref:`gmx angle `, :ref:`gmx covar `, + :ref:`gmx anaeig ` +| Principal component analysis can be performed in dihedral + space \ :ref:`172 ` using |Gromacs|. You start by defining the + dihedral angles of interest in an index file, either using + :ref:`gmx mk_angndx ` or otherwise. Then you use the + :ref:`gmx angle ` program with the ``-or`` flag to + produce a new :ref:`trr` file containing the cosine and sine + of each dihedral angle in two coordinates, respectively. That is, in + the :ref:`trr` file you will have a series of numbers + corresponding to: cos(\ :math:`\phi_1`), sin(\ :math:`\phi_1`), + cos(\ :math:`\phi_2`), sin(\ :math:`\phi_2`), ..., + cos(\ :math:`\phi_n`), sin(\ :math:`\phi_n`), and the array is padded + with zeros, if necessary. Then you can use this :ref:`trr` + file as input for the :ref:`gmx covar ` program and perform + principal component analysis as usual. For this to work you will need + to generate a reference file (:ref:`tpr`, + :ref:`gro`, :ref:`pdb` etc.) containing the same + number of “atoms” as the new :ref:`trr` file, that is for + :math:`n` dihedrals you need 2\ :math:`n`/3 atoms (rounded up if not + an integer number). You should use the ``-nofit`` option + for :ref:`gmx covar ` since the coordinates in the dummy + reference file do not correspond in any way to the information in the + :ref:`trr` file. Analysis of the results is done using + :ref:`gmx anaeig `. diff --git a/docs/reference-manual/analysis/dihedral-pca.rst b/docs/reference-manual/analysis/hydrogen-bonds.rst similarity index 68% copy from docs/reference-manual/analysis/dihedral-pca.rst copy to docs/reference-manual/analysis/hydrogen-bonds.rst index 8c31695026..c88f28479a 100644 --- a/docs/reference-manual/analysis/dihedral-pca.rst +++ b/docs/reference-manual/analysis/hydrogen-bonds.rst @@ -1,32 +1,3 @@ -Dihedral principal component analysis -------------------------------------- - -| :ref:`gmx angle `, :ref:`gmx covar `, - :ref:`gmx anaeig ` -| Principal component analysis can be performed in dihedral - space \ :ref:`172 ` using |Gromacs|. You start by defining the - dihedral angles of interest in an index file, either using - :ref:`gmx mk_angndx ` or otherwise. Then you use the - :ref:`gmx angle ` program with the ``-or`` flag to - produce a new :ref:`trr` file containing the cosine and sine - of each dihedral angle in two coordinates, respectively. That is, in - the :ref:`trr` file you will have a series of numbers - corresponding to: cos(\ :math:`\phi_1`), sin(\ :math:`\phi_1`), - cos(\ :math:`\phi_2`), sin(\ :math:`\phi_2`), ..., - cos(\ :math:`\phi_n`), sin(\ :math:`\phi_n`), and the array is padded - with zeros, if necessary. Then you can use this :ref:`trr` - file as input for the :ref:`gmx covar ` program and perform - principal component analysis as usual. For this to work you will need - to generate a reference file (:ref:`tpr`, - :ref:`gro`, :ref:`pdb` etc.) containing the same - number of “atoms” as the new :ref:`trr` file, that is for - :math:`n` dihedrals you need 2\ :math:`n`/3 atoms (rounded up if not - an integer number). You should use the ``-nofit`` option - for :ref:`gmx covar ` since the coordinates in the dummy - reference file do not correspond in any way to the information in the - :ref:`trr` file. Analysis of the results is done using - :ref:`gmx anaeig `. - Hydrogen bonds -------------- @@ -113,4 +84,3 @@ the following ways: donor-hydrogen atom pairs and acceptor atoms in these groups, donor-hydrogen-acceptor triplets involved in hydrogen bonds between the analyzed groups and all solvent atoms involved in insertion. - -- 2.11.4.GIT