From ec69db1f3dbeb03dbe5fed6785e6ebd5ccee4384 Mon Sep 17 00:00:00 2001 From: Giacomo Fiorin Date: Tue, 12 Mar 2024 16:49:03 -0400 Subject: [PATCH] Doc formatting minor fixes [update-doc] --- doc/colvars-refman-main.tex | 514 ++++++++++++++++++------------------ 1 file changed, 257 insertions(+), 257 deletions(-) diff --git a/doc/colvars-refman-main.tex b/doc/colvars-refman-main.tex index ecaaaeea5..d393b6cb7 100644 --- a/doc/colvars-refman-main.tex +++ b/doc/colvars-refman-main.tex @@ -97,49 +97,49 @@ The values of ``$c$''\cvnamebasedonly{ and ``alpha''} are also recorded throughout the simulation as a joint 2-dimensional histogram (see \ref{sec:colvarbias_histogram}). \begin{cvexampleinput} -colvar \{\\ -\-~~\# difference of two distances\\ -\-~~name d \\ -\-~~width 0.2 \# estimated fluctuation width \\ -\-~~distance \{\\ -\-~~~~componentCoeff 1.0\\ -\-~~~~group1 \{ atomNumbers 1 2 \}\\ -\-~~~~group2 \{ atomNumbers 3 4 5 \}\\ +colvar~\{\\ +\-~~\#~difference~of~two~distances\\ +\-~~name~d~\\ +\-~~width~0.2~~\#~estimated~fluctuation~width~\\ +\-~~distance~\{\\ +\-~~~~componentCoeff~~1.0\\ +\-~~~~group1~\{~atomNumbers~1~2~\}\\ +\-~~~~group2~\{~atomNumbers~3~4~5~\}\\ \-~~\}\\ -\-~~distance \{\\ -\-~~~~componentCoeff -1.0\\ -\-~~~~group1 \{ atomNumbers 7 \}\\ -\-~~~~group2 \{ atomNumbers 8 9 10 \}\\ +\-~~distance~\{\\ +\-~~~~componentCoeff~-1.0\\ +\-~~~~group1~\{~atomNumbers~7~\}\\ +\-~~~~group2~\{~atomNumbers~8~9~10~\}\\ \-~~\}\\ \}\\ \\ -colvar \{\\ -\-~~name c\\ -\-~~coordNum \{\\ -\-~~~~cutoff 6.0\\ -\-~~~~group1 \{ atomNumbersRange 1-10 \}\\ -\-~~~~group2 \{ atomNumbersRange 11-20 \}\\ -\-~~~~tolerance 1.0e-6\\ -\-~~~~pairListFrequency 1000\\ +colvar~\{\\ +\-~~name~c\\ +\-~~coordNum~\{\\ +\-~~~~cutoff~6.0\\ +\-~~~~group1~\{~atomNumbersRange~~1-10~\}\\ +\-~~~~group2~\{~atomNumbersRange~11-20~\}\\ +\-~~~~tolerance~1.0e-6\\ +\-~~~~pairListFrequency~1000\\ \-~~\}\\ \}\\ \cvnamebasedonly{% -colvar \{\\ -\-~~name alpha\\ -\-~~alpha \{\\ -\-~~~~psfSegID PROT\\ -\-~~~~residueRange 1-10\\ +colvar~\{\\ +\-~~name~alpha\\ +\-~~alpha~\{\\ +\-~~~~psfSegID~PROT\\ +\-~~~~residueRange~1-10\\ \-~~\}\\ \}} \\ -harmonic \{\\ -\-~~colvars d c\\ -\-~~centers 3.0 4.0\\ -\-~~forceConstant 5.0\\ +harmonic~\{\\ +\-~~colvars~d~c\\ +\-~~centers~3.0~4.0\\ +\-~~forceConstant~5.0\\ \}\\ \\ -histogram \{\\ -\-~~colvars c\cvnamebasedonly{ alpha}\\ +histogram~\{\\ +\-~~colvars~c\cvnamebasedonly{~alpha}\\ \} \end{cvexampleinput} @@ -313,7 +313,7 @@ Such a custom variable can either be computed on the fly (by calling an external tool or a VMD feature) or pre-computed and cached. For example, we can use VMD to compute the protein solvent-accessible surface area (SASA) on the fly: -\begin{cvexampleinput} +\begin{mdexampleinput} \-set~sasa\_sel~[atomselect~top~"protein~and~noh"]\\ \-\\ \-proc~calc\_user\_colvar~\{~x~\}~\{\\ @@ -321,7 +321,7 @@ \-~~\$::sasa\_sel~frame~[cv~frame]\\ \-~~return~[measure~sasa~1~\$::sasa\_sel]\\ \-\} -\end{cvexampleinput} +\end{mdexampleinput} The Tcl script above should be entered into VMD's text console, or sourced from a file. Then we can define a colvar that will be calculated by the scripted procedure above, by entering the following configuration as a new colvar in the Dashboad Editor Window: @@ -344,7 +344,7 @@ If the SASA computation is slow, it can be cached to make subsequent interaction responsive. To that effect, we source the following script to pre-compute the SASA for every frame and store it in VMD's User field for atom 0. -\begin{cvexampleinput} +\begin{mdexampleinput} \-set~atom0\_sel~[atomselect~top~"index~0"]\\ \-\\ \-for~\{set~f~0\}~\{\$f~<~[molinfo~top~get~numframes]\}~\{incr~f\}~\{\\ @@ -352,18 +352,18 @@ \-~~\$::atom0\_sel~frame~\$f\\ \-~~\$::atom0\_sel~set~user~[measure~sasa~1~\$::sasa\_sel]\\ \} -\end{cvexampleinput} +\end{mdexampleinput} Then we use the following Tcl procedure to compute a custom variable that is simply equal to the User field for atom 0 for the current frame: -\begin{cvexampleinput} +\begin{mdexampleinput} \-\\ \-proc~calc\_user\_colvar~\{~x~\}~\{\\ \-~~\#~Follow~current~Colvars~frame\\ \-~~\$::atom0\_sel~frame~[cv~frame]\\ \-~~return~[\$::atom0\_sel~get~user]\\ \-\} -\end{cvexampleinput} +\end{mdexampleinput} This version results in extremely fast updates. } % cvvmdonly dashboard @@ -1358,7 +1358,7 @@ A collective variable is defined by the keyword \texttt{colvar} followed by its configuration options contained within curly braces: \begin{cvexampleinput} -\-colvar \{\\ +\-colvar~\{\\ \-~~name~xi\\ \-~~$<$other~options$>$\\ \-~~function\_name~\{\\ @@ -3139,32 +3139,32 @@ The usage of \texttt{gzpath} and \texttt{gspath} is illustrated below: \begin{cvexampleinput} -colvar \{\\ -\-~~\# Progress along the path\\ -\-~~name gs\\ -\-~~\# The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)\\ -\-~~\# Use atomic coordinate from atoms 1, 2 and 3 to compute the path\\ -\-~~gspath \{\\ -\-~~~~atoms \{atomnumbers \{ 1 2 3 \}\}\\ -\-~~~~refPositionsFile1 string-00.pdb\\ -\-~~~~refPositionsFile2 string-01.pdb\\ -\-~~~~refPositionsFile3 string-02.pdb\\ -\-~~~~refPositionsFile4 string-03.pdb\\ -\-~~~~refPositionsFile5 string-04.pdb\\ +colvar~\{\\ +\-~~\#~Progress~along~the~path\\ +\-~~name~gs\\ +\-~~\#~The~path~is~defined~by~5~reference~frames~(from~string-00.pdb~to~string-04.pdb)\\ +\-~~\#~Use~atomic~coordinate~from~atoms~1,~2~and~3~to~compute~the~path\\ +\-~~gspath~\{\\ +\-~~~~atoms~\{atomnumbers~\{~1~2~3~\}\}\\ +\-~~~~refPositionsFile1~string-00.pdb\\ +\-~~~~refPositionsFile2~string-01.pdb\\ +\-~~~~refPositionsFile3~string-02.pdb\\ +\-~~~~refPositionsFile4~string-03.pdb\\ +\-~~~~refPositionsFile5~string-04.pdb\\ \-~~\}\\ \}\\ -\noindent\ttfamily colvar \{\\ -\-~~\# Distance from the path\\ -\-~~name gz\\ -\-~~\# The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)\\ -\-~~\# Use atomic coordinate from atoms 1, 2 and 3 to compute the path\\ -\-~~gzpath \{\\ -\-~~~~atoms \{atomnumbers \{ 1 2 3 \}\}\\ -\-~~~~refPositionsFile1 string-00.pdb\\ -\-~~~~refPositionsFile2 string-01.pdb\\ -\-~~~~refPositionsFile3 string-02.pdb\\ -\-~~~~refPositionsFile4 string-03.pdb\\ -\-~~~~refPositionsFile5 string-04.pdb\\ +\noindent\ttfamily~colvar~\{\\ +\-~~\#~Distance~from~the~path\\ +\-~~name~gz\\ +\-~~\#~The~path~is~defined~by~5~reference~frames~(from~string-00.pdb~to~string-04.pdb)\\ +\-~~\#~Use~atomic~coordinate~from~atoms~1,~2~and~3~to~compute~the~path\\ +\-~~gzpath~\{\\ +\-~~~~atoms~\{atomnumbers~\{~1~2~3~\}\}\\ +\-~~~~refPositionsFile1~string-00.pdb\\ +\-~~~~refPositionsFile2~string-01.pdb\\ +\-~~~~refPositionsFile3~string-02.pdb\\ +\-~~~~refPositionsFile4~string-03.pdb\\ +\-~~~~refPositionsFile5~string-04.pdb\\ \-~~\}\\ \} \end{cvexampleinput} @@ -3241,47 +3241,47 @@ The usage of \texttt{gzpathCV} and \texttt{gspathCV} is illustrated below: \begin{cvexampleinput} -\-colvar \{\\ -\-~~\# Progress along the path\\ -\-~~name gs\\ -\-~~\# Path defined by the CV space of two dihedral angles\\ -\-~~gspathCV \{\\ -\-~~~~pathFile ./path.txt\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 001\\ -\-~~~~~~group1 \{atomNumbers \{5\}\}\\ -\-~~~~~~group2 \{atomNumbers \{7\}\}\\ -\-~~~~~~group3 \{atomNumbers \{9\}\}\\ -\-~~~~~~group4 \{atomNumbers \{15\}\}\\ +\-colvar~\{\\ +\-~~\#~Progress~along~the~path\\ +\-~~name~gs\\ +\-~~\#~Path~defined~by~the~CV~space~of~two~dihedral~angles\\ +\-~~gspathCV~\{\\ +\-~~~~pathFile~./path.txt\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~001\\ +\-~~~~~~group1~\{atomNumbers~\{5\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{15\}\}\\ \-~~~~\}\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 002\\ -\-~~~~~~group1 \{atomNumbers \{7\}\}\\ -\-~~~~~~group2 \{atomNumbers \{9\}\}\\ -\-~~~~~~group3 \{atomNumbers \{15\}\}\\ -\-~~~~~~group4 \{atomNumbers \{17\}\}\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~002\\ +\-~~~~~~group1~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{15\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{17\}\}\\ \-~~~~\}\\ \-~~\}\\ \}\\ \\ -\-colvar \{\\ -\-~~\# Distance from the path\\ -\-~~name gz\\ -\-~~gzpathCV \{\\ -\-~~~~pathFile ./path.txt\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 001\\ -\-~~~~~~group1 \{atomNumbers \{5\}\}\\ -\-~~~~~~group2 \{atomNumbers \{7\}\}\\ -\-~~~~~~group3 \{atomNumbers \{9\}\}\\ -\-~~~~~~group4 \{atomNumbers \{15\}\}\\ +\-colvar~\{\\ +\-~~\#~Distance~from~the~path\\ +\-~~name~gz\\ +\-~~gzpathCV~\{\\ +\-~~~~pathFile~./path.txt\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~001\\ +\-~~~~~~group1~\{atomNumbers~\{5\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{15\}\}\\ \-~~~~\}\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 002\\ -\-~~~~~~group1 \{atomNumbers \{7\}\}\\ -\-~~~~~~group2 \{atomNumbers \{9\}\}\\ -\-~~~~~~group3 \{atomNumbers \{15\}\}\\ -\-~~~~~~group4 \{atomNumbers \{17\}\}\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~002\\ +\-~~~~~~group1~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{15\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{17\}\}\\ \-~~~~\}\\ \-~~\}\\ \} @@ -3362,51 +3362,51 @@ The usage of \texttt{azpathCV} and \texttt{aspathCV} is illustrated below: \begin{cvexampleinput} -colvar \{\\ -\-~~\# Progress along the path\\ -\-~~name as\\ -\-~~\# Path defined by the CV space of two dihedral angles\\ -\-~~aspathCV \{\\ -\-~~~~pathFile ./path.txt\\ -\-~~~~weights \{1.0 1.0\}\\ -\-~~~~lambda 0.005\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 001\\ -\-~~~~~~group1 \{atomNumbers \{5\}\}\\ -\-~~~~~~group2 \{atomNumbers \{7\}\}\\ -\-~~~~~~group3 \{atomNumbers \{9\}\}\\ -\-~~~~~~group4 \{atomNumbers \{15\}\}\\ +colvar~\{\\ +\-~~\#~Progress~along~the~path\\ +\-~~name~as\\ +\-~~\#~Path~defined~by~the~CV~space~of~two~dihedral~angles\\ +\-~~aspathCV~\{\\ +\-~~~~pathFile~./path.txt\\ +\-~~~~weights~\{1.0~1.0\}\\ +\-~~~~lambda~0.005\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~001\\ +\-~~~~~~group1~\{atomNumbers~\{5\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{15\}\}\\ \-~~~~\}\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 002\\ -\-~~~~~~group1 \{atomNumbers \{7\}\}\\ -\-~~~~~~group2 \{atomNumbers \{9\}\}\\ -\-~~~~~~group3 \{atomNumbers \{15\}\}\\ -\-~~~~~~group4 \{atomNumbers \{17\}\}\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~002\\ +\-~~~~~~group1~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{15\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{17\}\}\\ \-~~~~\}\\ \-~~\}\\ \}\\ \\ -colvar \{\\ -\-~~\# Distance from the path\\ -\-~~name az\\ -\-~~azpathCV \{\\ -\-~~~~pathFile ./path.txt\\ -\-~~~~weights \{1.0 1.0\}\\ -\-~~~~lambda 0.005\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 001\\ -\-~~~~~~group1 \{atomNumbers \{5\}\}\\ -\-~~~~~~group2 \{atomNumbers \{7\}\}\\ -\-~~~~~~group3 \{atomNumbers \{9\}\}\\ -\-~~~~~~group4 \{atomNumbers \{15\}\}\\ +colvar~\{\\ +\-~~\#~Distance~from~the~path\\ +\-~~name~az\\ +\-~~azpathCV~\{\\ +\-~~~~pathFile~./path.txt\\ +\-~~~~weights~\{1.0~1.0\}\\ +\-~~~~lambda~0.005\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~001\\ +\-~~~~~~group1~\{atomNumbers~\{5\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{15\}\}\\ \-~~~~\}\\ -\-~~~~dihedral \{\\ -\-~~~~~~name 002\\ -\-~~~~~~group1 \{atomNumbers \{7\}\}\\ -\-~~~~~~group2 \{atomNumbers \{9\}\}\\ -\-~~~~~~group3 \{atomNumbers \{15\}\}\\ -\-~~~~~~group4 \{atomNumbers \{17\}\}\\ +\-~~~~dihedral~\{\\ +\-~~~~~~name~002\\ +\-~~~~~~group1~\{atomNumbers~\{7\}\}\\ +\-~~~~~~group2~\{atomNumbers~\{9\}\}\\ +\-~~~~~~group3~\{atomNumbers~\{15\}\}\\ +\-~~~~~~group4~\{atomNumbers~\{17\}\}\\ \-~~~~\}\\ \-~~\}\\ \} @@ -3503,32 +3503,33 @@ The usage of \texttt{azpath} and \texttt{aspath} is illustrated below: \begin{cvexampleinput} -colvar \{\\ -\-~~\# Progress along the path\\ -\-~~name as\\ -\-~~\# The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)\\ -\-~~\# Use atomic coordinate from atoms 1, 2 and 3 to compute the path\\ -\-~~aspath \{\\ -\-~~~~atoms \{atomnumbers \{ 1 2 3 \}\}\\ -\-~~~~refPositionsFile1 string-00.pdb\\ -\-~~~~refPositionsFile2 string-01.pdb\\ -\-~~~~refPositionsFile3 string-02.pdb\\ -\-~~~~refPositionsFile4 string-03.pdb\\ -\-~~~~refPositionsFile5 string-04.pdb\\ +\-colvar~\{\\ +\-~~\#~Progress~along~the~path\\ +\-~~name~as\\ +\-~~\#~The~path~is~defined~by~5~reference~frames~(from~string-00.pdb~to~string-04.pdb)\\ +\-~~\#~Use~atomic~coordinate~from~atoms~1,~2~and~3~to~compute~the~path\\ +\-~~aspath~\{\\ +\-~~~~atoms~\{atomnumbers~\{~1~2~3~\}\}\\ +\-~~~~refPositionsFile1~string-00.pdb\\ +\-~~~~refPositionsFile2~string-01.pdb\\ +\-~~~~refPositionsFile3~string-02.pdb\\ +\-~~~~refPositionsFile4~string-03.pdb\\ +\-~~~~refPositionsFile5~string-04.pdb\\ \-~~\}\\ -\}\\ -\noindent\ttfamily colvar \{\\ -\-~~\# Distance from the path\\ -\-~~name az\\ -\-~~\# The path is defined by 5 reference frames (from string-00.pdb to string-04.pdb)\\ -\-~~\# Use atomic coordinate from atoms 1, 2 and 3 to compute the path\\ -\-~~azpath \{\\ -\-~~~~atoms \{atomnumbers \{ 1 2 3 \}\}\\ -\-~~~~refPositionsFile1 string-00.pdb\\ -\-~~~~refPositionsFile2 string-01.pdb\\ -\-~~~~refPositionsFile3 string-02.pdb\\ -\-~~~~refPositionsFile4 string-03.pdb\\ -\-~~~~refPositionsFile5 string-04.pdb\\ +\-\}\\ +\-\\ +\-colvar~\{\\ +\-~~\#~Distance~from~the~path\\ +\-~~name~az\\ +\-~~\#~The~path~is~defined~by~5~reference~frames~(from~string-00.pdb~to~string-04.pdb)\\ +\-~~\#~Use~atomic~coordinate~from~atoms~1,~2~and~3~to~compute~the~path\\ +\-~~azpath~\{\\ +\-~~~~atoms~\{atomnumbers~\{~1~2~3~\}\}\\ +\-~~~~refPositionsFile1~string-00.pdb\\ +\-~~~~refPositionsFile2~string-01.pdb\\ +\-~~~~refPositionsFile3~string-02.pdb\\ +\-~~~~refPositionsFile4~string-03.pdb\\ +\-~~~~refPositionsFile5~string-04.pdb\\ \-~~\}\\ \} \end{cvexampleinput} @@ -4055,22 +4056,22 @@ A vector variable may be defined by specifying the \texttt{customFunction} parameter several times: each expression defines one scalar element of the vector colvar, as in this example: \begin{cvexampleinput} -\-colvar \{\\ -\-~~name custom\\ +\-colvar~\{\\ +\-~~name~custom\\ \\ -\-~~\# A 2-dimensional vector function of a scalar x and a 3-vector r\\ -\-~~customFunction cos(x) * (r1 + r2 + r3)\\ -\-~~customFunction sqrt(r1 * r2)\\ +\-~~\#~A~2-dimensional~vector~function~of~a~scalar~x~and~a~3-vector~r\\ +\-~~customFunction~cos(x)~*~(r1~+~r2~+~r3)\\ +\-~~customFunction~sqrt(r1~*~r2)\\ \\ -\-~~distance \{\\ -\-~~~~name x\\ -\-~~~~group1 \{ atomNumbers 1 \}\\ -\-~~~~group2 \{ atomNumbers 50 \}\\ +\-~~distance~\{\\ +\-~~~~name~x\\ +\-~~~~group1~\{~atomNumbers~1~\}\\ +\-~~~~group2~\{~atomNumbers~50~\}\\ \-~~\}\\ -\-~~distanceVec \{\\ -\-~~~~name r\\ -\-~~~~group1 \{ atomNumbers 10 11 12 \}\\ -\-~~~~group2 \{ atomNumbers 20 21 22 \}\\ +\-~~distanceVec~\{\\ +\-~~~~name~r\\ +\-~~~~group1~\{~atomNumbers~10~11~12~\}\\ +\-~~~~group2~\{~atomNumbers~~20~21~22~\}\\ \-~~\}\\ \} \end{cvexampleinput} @@ -4723,28 +4724,28 @@ \textbf{Note: }\emph{this is an unusually varied combination of selection keywords, demonstrating how they can be combined together: most simulations only use one of them.}\\ \begin{cvexampleinput} -\-atoms \{\\ +\-atoms~\{\\ \\ -\-~~\# add atoms 1 and 3 to this group (note: first atom in the system is 1)\\ -\-~~atomNumbers \{ \\ -\-~~~~1 3\\ +\-~~\#~add~atoms~1~and~3~to~this~group~(note:~first~atom~in~the~system~is~1)\\ +\-~~atomNumbers~\{~\\ +\-~~~~1~3\\ \-~~\}\\ \\ -\-~~\# add atoms starting from 20 up to and including 50\\ -\-~~atomNumbersRange 20-50\\ +\-~~\#~add~atoms~starting~from~20~up~to~and~including~50\\ +\-~~atomNumbersRange~~20-50\\ \cvnamebasedonly{% -\-~~\# add all the atoms with occupancy 2 in the file atoms.pdb\\ -\-~~atomsFile atoms.pdb\\ -\-~~atomsCol O\\ -\-~~atomsColValue 2.0\\ +\-~~\#~add~all~the~atoms~with~occupancy~2~in~the~file~atoms.pdb\\ +\-~~atomsFile~~~~~~~~~~~~~atoms.pdb\\ +\-~~atomsCol~~~~~~~~~~~~~~O\\ +\-~~atomsColValue~~~~~~~~~2.0\\ \\ -\-~~\# add all the C-alphas within residues 11 to 20 of segments "PR1" and "PR2"\\ -\-~~psfSegID PR1 PR2\\ -\-~~atomNameResidueRange CA 11-20\\ -\-~~atomNameResidueRange CA 11-20\\ +\-~~\#~add~all~the~C-alphas~within~residues~11~to~20~of~segments~"PR1"~and~"PR2"\\ +\-~~psfSegID~~~~~~~~~~~~~~PR1~PR2\\ +\-~~atomNameResidueRange~~CA~11-20\\ +\-~~atomNameResidueRange~~CA~11-20\\ } -\-~~\# add index group (requires a .ndx file to be provided globally)\\ -\-~~indexGroup Water\\ +\-~~\#~add~index~group~(requires~a~.ndx~file~to~be~provided~globally)\\ +\-~~indexGroup~Water\\ \} \end{cvexampleinput} @@ -4992,22 +4993,22 @@ To define a DBC coordinate, this atom group would be used within an \refkey{rmsd}{sec:cvc_rmsd} function. \begin{cvexampleinput} -\-\# Example: defining a group "atoms" (the ligand) whose coordinates are expressed \\ -\# in a roto-translated frame of reference defined by a second group (the receptor)\\ -atoms \{\\ +\-\#~Example:~defining~a~group~"atoms"~(the~ligand)~whose~coordinates~are~expressed~\\ +\#~in~a~roto-translated~frame~of~reference~defined~by~a~second~group~(the~receptor)\\ +atoms~\{\\ \\ -\-~~atomNumbers 1 2 3 4 5 6 7 \# atoms of the ligand (1-based)\\ +\-~~atomNumbers~1~2~3~4~5~6~7~\#~atoms~of~the~ligand~(1-based)\\ \\ -\-~~centerToReference yes\\ -\-~~rotateToReference yes\\ -\-~~fittingGroup \{\\ -\-~~~~\# define the frame by fitting alpha carbon atoms\\ -\-~~~~\# in 2 protein segments close to the site\\ -\-~~~~psfSegID PROT PROT\\ -\-~~~~atomNameResidueRange CA 1-40\\ -\-~~~~atomNameResidueRange CA 59-100\\ -\-~~\} \\ -\-~~refPositionsFile all.pdb \# can be the entire system\\ +\-~~centerToReference~yes\\ +\-~~rotateToReference~yes\\ +\-~~fittingGroup~\{\\ +\-~~~~\#~define~the~frame~by~fitting~alpha~carbon~atoms\\ +\-~~~~\#~in~2~protein~segments~close~to~the~site\\ +\-~~~~psfSegID~~~~~~~~~~~~~~PROT~PROT\\ +\-~~~~atomNameResidueRange~~CA~1-40\\ +\-~~~~atomNameResidueRange~~CA~59-100\\ +\-~~\}~\\ +\-~~refPositionsFile~all.pdb~~\#~can~be~the~entire~system\\ \} \end{cvexampleinput} } @@ -5123,7 +5124,6 @@ A biasing or analysis method can be applied to existing collective variables by using the following configuration: \begin{cvexampleinput} - \-$<$biastype$>$~\{\\ \-~~name~$<$name$>$ \\ \-~~colvars~$<$xi1$>$~$<$xi2$>$~...\\ @@ -5960,25 +5960,25 @@ \noindent\textbf{Example:} Using harmonic walls to protect the grid's boundaries. \begin{cvexampleinput} -\-colvar \{\\ -\-\-~~name r\\ -\-\-~~distance \{ ... \}\\ -\-\-~~upperBoundary 15.0\\ -\-\-~~width 0.2\\ +\-colvar~\{\\ +\-\-~~name~r\\ +\-\-~~distance~\{~...~\}\\ +\-\-~~upperBoundary~15.0\\ +\-\-~~width~0.2\\ \-\}\\ \\ -\-metadynamics \{\\ -\-\-~~name meta\_r\\ -\-\-~~colvars r\\ -\-\-~~hillWeight 0.001\\ -\-\-~~hillWidth 2.0\\ +\-metadynamics~\{\\ +\-\-~~name~meta\_r\\ +\-\-~~colvars~r\\ +\-\-~~hillWeight~0.001\\ +\-\-~~hillWidth~2.0\\ \-\}\\ \\ -\-harmonicWalls \{\\ -\-\-~~name wall\_r\\ -\-\-~~colvars r\\ -\-\-~~upperWalls 13.0\\ -\-\-~~upperWallConstant 2.0\\ +\-harmonicWalls~\{\\ +\-\-~~name~wall\_r\\ +\-\-~~colvars~r\\ +\-\-~~upperWalls~13.0\\ +\-\-~~upperWallConstant~2.0\\ \-\} \end{cvexampleinput} @@ -6261,24 +6261,24 @@ \noindent\textbf{Example:} EBmetaD configuration for a single variable. \begin{cvexampleinput} -\-colvar \{\\ -\-\-~~name r \\ -\-\-~~distance \{\\ -\-\-~~~~group1 \{ atomNumbers 991 992 \}\\ -\-\-~~~~group2 \{ atomNumbers 1762 1763 \}\\ +\-colvar~\{\\ +\-\-~~name~r~\\ +\-\-~~distance~\{\\ +\-\-~~~~group1~\{~atomNumbers~991~992~\}\\ +\-\-~~~~group2~\{~atomNumbers~1762~1763~\}\\ \-\-~~\}\\ -\-\-~~upperBoundary 100.0 \\ -\-\-~~width 0.1 \\ +\-\-~~upperBoundary~~100.0~\\ +\-\-~~width~~~~~~~~~~~~0.1~\\ \-\}\\ \\ -\-metadynamics \{\\ -\-\-~~name ebmeta\\ -\-\-~~colvars r\\ -\-\-~~hillWeight 0.01\\ -\-\-~~hillWidth 3.0\\ -\-\-~~ebMeta on\\ -\-\-~~targetDistFile targetdist1.dat\\ -\-\-~~ebMetaEquilSteps 500000\\ +\-metadynamics~\{\\ +\-\-~~name~~~~~~~~~~~~~~ebmeta\\ +\-\-~~colvars~~~~~~~~~~~r\\ +\-\-~~hillWeight~~~~~~~~0.01\\ +\-\-~~hillWidth~~~~~~~~~3.0\\ +\-\-~~ebMeta~~~~~~~~~~~~on\\ +\-\-~~targetDistFile~~~~targetdist1.dat\\ +\-\-~~ebMetaEquilSteps~~500000\\ \-\} \end{cvexampleinput} @@ -6353,16 +6353,16 @@ \noindent\textbf{Example:} Multiple-walker metadynamics with file-based communication.\\ \begin{cvexampleinput} -\-metadynamics \{\\ -\-\-~~name mymtd\\ -\-\-~~colvars x\\ -\-\-~~hillWeight 0.001\\ -\-\-~~newHillFrequency 1000\\ -\-\-~~hillWidth 3.0\\ +\-metadynamics~\{\\ +\-\-~~name~mymtd\\ +\-\-~~colvars~x\\ +\-\-~~hillWeight~0.001\\ +\-\-~~newHillFrequency~1000\\ +\-\-~~hillWidth~3.0\\ \-\-~~\\ -\-\-~~multipleReplicas on\\ -\-\-~~replicasRegistry /shared-folder/mymtd-replicas.txt\\ -\-\-~~replicaUpdateFrequency 50000 \# Best if larger than newHillFrequency\\ +\-\-~~multipleReplicas~~~~~~~on\\ +\-\-~~replicasRegistry~~~~~~~/shared-folder/mymtd-replicas.txt\\ +\-\-~~replicaUpdateFrequency~50000~~\#~Best~if~larger~than~newHillFrequency\\ \-\} \end{cvexampleinput} @@ -6817,24 +6817,24 @@ \noindent\textbf{Example 1:} harmonic walls for one variable with two different force constants. \begin{cvexampleinput} -\-harmonicWalls \{\\ -\-\-~~name mywalls\\ -\-\-~~colvars dist\\ -\-\-~~lowerWalls 22.0 \\ -\-\-~~upperWalls 38.0 \\ -\-\-~~lowerWallConstant 2.0 \\ -\-\-~~upperWallConstant 10.0 \\ +\-harmonicWalls~\{\\ +\-\-~~name~~mywalls\\ +\-\-~~colvars~~~~dist\\ +\-\-~~lowerWalls~~22.0~\\ +\-\-~~upperWalls~~38.0~\\ +\-\-~~lowerWallConstant~~2.0~\\ +\-\-~~upperWallConstant~10.0~\\ \-\} \end{cvexampleinput} \noindent\textbf{Example 2:} harmonic walls for two variables with a single force constant. \begin{cvexampleinput} -\-harmonicWalls \{\\ -\-\-~~name mywalls\\ -\-\-~~colvars phi psi\\ -\-\-~~lowerWalls -180.0 0.0\\ -\-\-~~upperWalls 0.0 180.0\\ -\-\-~~forceConstant 5.0 \\ +\-harmonicWalls~\{\\ +\-\-~~name~~mywalls\\ +\-\-~~colvars~~~~~~~phi~~~~psi\\ +\-\-~~lowerWalls~-180.0~~~~0.0\\ +\-\-~~upperWalls~~~~0.0~~180.0\\ +\-\-~~forceConstant~5.0~\\ \-\} \end{cvexampleinput}