diff --git a/doc/CpptrajManual.pdf b/doc/CpptrajManual.pdf index 9538085a43..e15bf8b5af 100644 Binary files a/doc/CpptrajManual.pdf and b/doc/CpptrajManual.pdf differ diff --git a/doc/DocumentChecksums.txt b/doc/DocumentChecksums.txt index 9bf71d8580..442368867c 100644 --- a/doc/DocumentChecksums.txt +++ b/doc/DocumentChecksums.txt @@ -1,3 +1,3 @@ b37726e7a841f6fc695ecd7fb040ffbf CpptrajDevelopmentGuide.lyx -1f4d9c647b6717314560290a4d3f9f06 cpptraj.lyx +a39607942c916369bcba6dfa9109f18b cpptraj.lyx 5d9b5b5ed47a3ded57b6464df99b3585 CpptrajManual.lyx diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx index ef80cacef0..153d257ede 100644 --- a/doc/cpptraj.lyx +++ b/doc/cpptraj.lyx @@ -1,4 +1,4 @@ -#LyX 2.4 created this file. For more info see https://www.lyx.org/ +#LyX 2.3 created this file. For more info see http://www.lyx.org/ \lyxformat 544 \begin_document \begin_header @@ -117,14 +117,15 @@ literal "true" \emph on ptraj \emph default -) is the main program in Amber for processing coordinate trajectories and data files. +) is the main program in Amber for processing coordinate trajectories and + data files. \shape italic Cpptraj \shape default - has a wide range of functionality, - and makes use of OpenMP/MPI to speed up many calculations, - including processing ensembles of trajectories and/or conducting multiple analyses in parallel with MPI. + has a wide range of functionality, and makes use of OpenMP/MPI to speed + up many calculations, including processing ensembles of trajectories and/or + conducting multiple analyses in parallel with MPI. \begin_inset CommandInset citation LatexCommand citep key "Roe2018" @@ -152,8 +153,7 @@ Several actions/analyses in \emph on cpptraj \emph default - are OpenMP parallelized; - see section + are OpenMP parallelized; see section \begin_inset CommandInset ref LatexCommand ref reference "subsec:CpptrajOpenMP" @@ -173,30 +173,30 @@ Almost any file read or written by cpptraj \emph default can be compressed (with the exception of the NetCDF trajectory format). - So for example gzipped/bzipped topology files can be read, - and data files can be written out as gzip/bzip2 files. - Compression is detected automatically when reading, - and is determined by the filename extension (.gz and .bz2 respectively) on writing. + So for example gzipped/bzipped topology files can be read, and data files + can be written out as gzip/bzip2 files. + Compression is detected automatically when reading, and is determined by + the filename extension (.gz and .bz2 respectively) on writing. \end_layout \begin_layout Enumerate The format of output data files can be specified by extension. - For example, - data files can be written in xmgrace format if the filename given has a '.agr' extension. + For example, data files can be written in xmgrace format if the filename + given has a '.agr' extension. A trajectory can be written in DCD format if the '.dcd' extension is used. \end_layout \begin_layout Enumerate -Multiple output trajectories can be specified, - and can be written during action processing (as opposed to only after) via the +Multiple output trajectories can be specified, and can be written during + action processing (as opposed to only after) via the \series bold \shape italic outtraj \series default \shape default command. - In addition, - output files can be directed to write only specific frames from the input trajectories. + In addition, output files can be directed to write only specific frames + from the input trajectories. \end_layout \begin_layout Enumerate @@ -212,8 +212,7 @@ rmsd \series default \shape default action allows specification of a separate mask for the reference structure. - In addition, - per-residue RMSD can be calculated easily. + In addition, per-residue RMSD can be calculated easily. \end_layout @@ -230,12 +229,14 @@ strip closest \series default \shape default - actions can often write an accompanying fully-functional stripped topology file. + actions can often write an accompanying fully-functional stripped topology + file. \end_layout \begin_layout Enumerate -Users usually are able to fine-tune the output format of data files declared in actions using the +Users usually are able to fine-tune the output format of data files declared + in actions using the \begin_inset Quotes eld \end_inset @@ -247,17 +248,16 @@ out \begin_inset Quotes erd \end_inset - keyword (for example, - the precision of the numbers can be changed). - In addition, - users can control which data sets are written to which files (e.g. - if two actions specify the same data file with the 'out' keyword, - data from both actions will be written to that data file). + keyword (for example, the precision of the numbers can be changed). + In addition, users can control which data sets are written to which files + (e.g. + if two actions specify the same data file with the 'out' keyword, data + from both actions will be written to that data file). \end_layout \begin_layout Enumerate -Users can manipulate data sets using mathematical expressions (with some limitations), - see +Users can manipulate data sets using mathematical expressions (with some + limitations), see \begin_inset CommandInset ref LatexCommand vref reference "subsec:cpptraj-Data-Set-Math" @@ -275,15 +275,13 @@ There is some support for creating internal loops over e.g. for \series default \emph default -, - +, \series bold \emph on set \series default \emph default -, - and +, and \series bold \emph on show @@ -297,9 +295,7 @@ See the README.md file in the \emph on cpptraj \emph default - home directory for information on how to build, - authors, - and so on. + home directory for information on how to build, authors, and so on. \end_layout \begin_layout Subsection @@ -319,8 +315,8 @@ The syntax presented in this manual uses the following conventions: \end_layout \begin_layout Description -{|} Denotes several choices separated by the '|' character; - one of the choices must be specified. +{|} Denotes several choices separated by the '|' character; one of the choices + must be specified. \end_layout \begin_layout Description @@ -338,8 +334,8 @@ Installation \end_layout \begin_layout Standard -See instructions in the CPPTRAJ GitHub repository README.md file under 'Installation & Testing': - +See instructions in the CPPTRAJ GitHub repository README.md file under 'Installat +ion & Testing': \begin_inset Flex URL status open @@ -465,8 +461,7 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -* Read from trajectory file ; - same as input 'trajin '. +* Read from trajectory file ; same as input 'trajin '. \end_layout \begin_layout Description @@ -474,8 +469,7 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -* Write trajectory file ; - same as input 'trajout '. +* Write trajectory file ; same as input 'trajout '. \end_layout \begin_layout Description @@ -495,9 +489,7 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \end_layout \begin_layout Description -* A topology, - input trajectory, - or file containing cpptraj input. +* A topology, input trajectory, or file containing cpptraj input. \end_layout \begin_layout Description @@ -505,8 +497,8 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -* Read as reference coordinates; - same as input 'reference '. +* Read as reference coordinates; same as input 'reference + '. \end_layout \begin_layout Description @@ -566,8 +558,7 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset -<#> Set global debug level to <#>; - same as input 'debug <#>'. +<#> Set global debug level to <#>; same as input 'debug <#>'. \end_layout \begin_layout Description @@ -585,8 +576,7 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_layout Description -tl Print length of trajectories specified with '-y' to STDOUT. - The total number of frames is written out as 'Frames: - ' + The total number of frames is written out as 'Frames: ' \end_layout \begin_layout Description @@ -603,8 +593,7 @@ cpptraj [-p ] [-i ] [-y ] [-x ] \begin_inset space ~ \end_inset - : - Print selected residue numbers to STDOUT. + : Print selected residue numbers to STDOUT. Selected residues are written out as 'Selected= 1 2 3 ...' \end_layout @@ -646,13 +635,14 @@ Note that unlike \shape italic ptraj \shape default -, - in +, in \shape italic cpptraj \shape default - it is not required that a topology file be specified on the command line as long as one is specified in the input file with the 'parm' keyword. - Multiple topology/input files can be specified by use of multiple '-p' and '-i' flags. + it is not required that a topology file be specified on the command line + as long as one is specified in the input file with the 'parm' keyword. + Multiple topology/input files can be specified by use of multiple '-p' + and '-i' flags. All topology and coordinate flags will be processed before any input flags. \end_layout @@ -665,12 +655,11 @@ Input to \shape italic cpptraj \shape default - is in the form of commands, - which can be categorized in to 2 types: - immediate and queued. + is in the form of commands, which can be categorized in to 2 types: immediate + and queued. Immediate commands are executed as soon as they are encountered. - Queued commands are initialized when they are encountered, - but are not executed until a Run is executed via a + Queued commands are initialized when they are encountered, but are not + executed until a Run is executed via a \series bold \shape italic run @@ -683,23 +672,19 @@ go \series default \shape default command. - Actions, - Analyses, - and Trajectory commands (except + Actions, Analyses, and Trajectory commands (except \series bold \emph on reference \series default \emph default -) are queued commands; - however, - they can also be run immediately via commands such as +) are queued commands; however, they can also be run immediately via commands + such as \series bold \shape italic crdaction \series default , - \shape default \series bold @@ -707,7 +692,6 @@ crdaction runanalysis \series default , - \shape default \series bold @@ -715,8 +699,7 @@ runanalysis loadcrd \series default \emph default -, - etc. +, etc. See \begin_inset CommandInset ref LatexCommand vref @@ -737,9 +720,7 @@ General (Immediate) These commands are executed immediately when entered. \begin_layout Description System (Immediate) These are unix system commands (e.g. - 'ls', - 'pwd', - etc). + 'ls', 'pwd', etc). \end_layout \begin_layout Description @@ -755,36 +736,39 @@ reference "sec:Coordinates-as-a" \end_layout \begin_layout Description -Trajectory (Queued) These commands prepare cpptraj for reading or writing trajectories during a Run. +Trajectory (Queued) These commands prepare cpptraj for reading or writing + trajectories during a Run. \end_layout \begin_layout Description -Topology (Immediate) These commands are used to read, - write, - and modify topology information. +Topology (Immediate) These commands are used to read, write, and modify + topology information. \end_layout \begin_layout Description -Action (Queued) These commands specify actions that will be performed on coordinate frames read in from trajectories during a Run. +Action (Queued) These commands specify actions that will be performed on + coordinate frames read in from trajectories during a Run. \end_layout \begin_layout Description -Analysis (Queued) These commands specify analyses that will be performed on data that has been either generated from a Run or read in from an external source. +Analysis (Queued) These commands specify analyses that will be performed + on data that has been either generated from a Run or read in from an external + source. \end_layout \begin_layout Description -Control (Immediate) These commands set up control blocks that can be used to e.g. +Control (Immediate) These commands set up control blocks that can be used + to e.g. loop over a set of commands. \end_layout \begin_layout Standard -In addition to normal commands, - +In addition to normal commands, \emph on cpptraj \emph default - now has the ability to perform certain basic math operations, - even on data sets. + now has the ability to perform certain basic math operations, even on data + sets. See \begin_inset CommandInset ref LatexCommand vref @@ -801,13 +785,12 @@ Commands in cpptraj \shape default can be read in from an input file or from the interactive command prompt. - A '#' anywhere on a line denotes a comment; - anything after '#' will be ignored no matter where it occurs. + A '#' anywhere on a line denotes a comment; anything after '#' will be + ignored no matter where it occurs. A ' \backslash ' allows the continuation of one line to another. - For example, - the input: + For example, the input: \end_layout \begin_layout LyX-Code @@ -845,11 +828,13 @@ Getting Help \end_layout \begin_layout Standard -If in interactive mode, - the 'help' command can be used to list recognized commands and topics; - topics (such as mask syntax) start with uppercase letters. - 'help ' can be used to get the associated keywords as well as an abbreviated description of the command. - Most commands have a corresponding test which also serves as an example of how to use the command. +If in interactive mode, the 'help' command can be used to list recognized + commands and topics; topics (such as mask syntax) start with uppercase + letters. + 'help ' can be used to get the associated keywords as well as + an abbreviated description of the command. + Most commands have a corresponding test which also serves as an example + of how to use the command. See $AMBERHOME/AmberTools/test/cpptraj/README for more details. \end_layout @@ -866,8 +851,8 @@ batch \begin_inset Quotes erd \end_inset - mode, - cpptraj is executed from the command line with one or more input files containing commands to be processed or STDIN. + mode, cpptraj is executed from the command line with one or more input + files containing commands to be processed or STDIN. The syntax of is similar to that of \shape italic ptraj @@ -895,14 +880,13 @@ interactive mode \end_inset users can enter commands in a UNIX-like shell. - Interactive mode is useful for running short and simple analyses or for trying out new kinds of analyses. + Interactive mode is useful for running short and simple analyses or for + trying out new kinds of analyses. If \emph on cpptraj \emph default - is run with '–interactive', - no arguments, - or no specified input file: + is run with '–interactive', no arguments, or no specified input file: \end_layout \begin_layout LyX-Code @@ -923,12 +907,13 @@ cpptraj -p \begin_layout Standard this brings up the interactive interface. - This interface supports command history (via the up and down arrows) and tab completion for commands and file names. - If no log file name has been given (with '–log '), - all commands used in interactive mode will be logged to a file named 'cpptraj.log', - which can subsequently be used as input if desired. - When starting cpptraj, - command histories will be read from any existing logs. + This interface supports command history (via the up and down arrows) and + tab completion for commands and file names. + If no log file name has been given (with '–log '), all commands + used in interactive mode will be logged to a file named 'cpptraj.log', which + can subsequently be used as input if desired. + When starting cpptraj, command histories will be read from any existing + logs. \end_layout \begin_layout Subsection @@ -948,8 +933,7 @@ Like \shape italic ptraj \shape default -, - a trajectory processing +, a trajectory processing \begin_inset Quotes eld \end_inset @@ -962,13 +946,14 @@ Run cpptraj \shape default . - First the Run is set up via commands read in from an input file or the interactive prompt. - Trajectories are then read in one frame at a time (or in the case of ensemble processing all frames from a given step are read). - Actions are performed on the coordinates stored in the frame, - after which any output coordinates are written. - At the end of the run, - any data sets generated are written, - and any queued Analyses are performed. + First the Run is set up via commands read in from an input file or the + interactive prompt. + Trajectories are then read in one frame at a time (or in the case of ensemble + processing all frames from a given step are read). + Actions are performed on the coordinates stored in the frame, after which + any output coordinates are written. + At the end of the run, any data sets generated are written, and any queued + Analyses are performed. \end_layout \begin_layout Subsubsection @@ -980,12 +965,14 @@ Since \emph on cpptraj \emph default - supports multiple topology files, - during a Run actions are set up every time the topology changes in order to recalculate things like what atoms are in a mask etc. - Actions that are not valid for the current topology are skipped for that topology. - So for example given two topology files with 100 residues, - if the first topology file processed includes a ligand named MOL and the second one does not, - the action: + supports multiple topology files, during a Run actions are set up every + time the topology changes in order to recalculate things like what atoms + are in a mask etc. + Actions that are not valid for the current topology are skipped for that + topology. + So for example given two topology files with 100 residues, if the first + topology file processed includes a ligand named MOL and the second one + does not, the action: \end_layout \begin_layout LyX-Code @@ -993,8 +980,8 @@ distance :80 :MOL out D_80-to-MOL.dat \end_layout \begin_layout Standard -will be valid for the first topology but not for the second, - so it will be skipped as long as the second topology is active. +will be valid for the first topology but not for the second, so it will + be skipped as long as the second topology is active. \end_layout \begin_layout Subsection @@ -1007,22 +994,20 @@ Parallelization Cpptraj \emph default has many levels of parallelization that can be enabled via the '-mpi', - '-openmp', - and/or '-cuda' configure flags for MPI, - OpenMP, - and CUDA parallelization respectively. - At the highest level, - trajectory and ensemble reads are parallelized with MPI. - In addition, - certain time consuming actions have been parallelized with OpenMP and/or CUDA. + '-openmp', and/or '-cuda' configure flags for MPI, OpenMP, and CUDA paralleliza +tion respectively. + At the highest level, trajectory and ensemble reads are parallelized with + MPI. + In addition, certain time consuming actions have been parallelized with + OpenMP and/or CUDA. \end_layout \begin_layout Standard -Note that any combination of the '-openmp', - '-cuda', - and '-mpi' flags may be used to generate a hybrid MPI/OpenMP/CUDA binary; - however this may require additional runtime setup (e.g. - setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe cores. +Note that any combination of the '-openmp', '-cuda', and '-mpi' flags may + be used to generate a hybrid MPI/OpenMP/CUDA binary; however this may require + additional runtime setup (e.g. + setting OMP_NUM_THREADS for OpenMP) to work properly and not oversubscribe + cores. \end_layout \begin_layout Subsubsection @@ -1048,72 +1033,62 @@ Cpptraj trajin \series default \emph default -' trajectory input, - where the trajectory read is divided as evenly as possible among all input frames (across-trajectory parallelism). - For example, - if given two trajectories of 1000 frames each and 4 MPI processes, - process 0 reads frames 1-500 of trajectory 1, - process 1 reads frames 501-1000 of trajectory 1, - process 2 reads frames 1-500 of trajectory 2, - and process 3 reads frames 501-1000 of trajectory 2. - Most Actions will work with across-trajectory parallelization with the exception of the following: - +' trajectory input, where the trajectory read is divided as evenly as possible + among all input frames (across-trajectory parallelism). + For example, if given two trajectories of 1000 frames each and 4 MPI processes, + process 0 reads frames 1-500 of trajectory 1, process 1 reads frames 501-1000 + of trajectory 1, process 2 reads frames 1-500 of trajectory 2, and process + 3 reads frames 501-1000 of trajectory 2. + Most Actions will work with across-trajectory parallelization with the + exception of the following: \series bold \emph on 'clusterdihedral' \series default \emph default -, - +, \series bold \emph on 'contacts' \series default \emph default -, - +, \series bold \emph on 'createreservoir' \series default \emph default -, - +, \series bold \emph on 'lipidorder' \series default \emph default -, - +, \series bold \emph on 'pairwise' \series default \emph default -, - +, \series bold \emph on 'stfcdiffusion' \series default \emph default -, - +, \series bold \emph on 'tordiff' \series default \emph default -, - +, \series bold \emph on 'unwrap' \series default \emph default -, - and +, and \series bold \emph on 'xtalsymm' @@ -1126,18 +1101,19 @@ trajin 'diffusion' \series default \emph default - Action will only work with across-trajectory parallelism if no imaging is to be performed. + Action will only work with across-trajectory parallelism if no imaging + is to be performed. \end_layout \begin_layout Standard -In addition to across-trajectory parallelism, - the +In addition to across-trajectory parallelism, the \series bold \emph on 'gist' \series default \emph default - command will also MPI-parallelize the entropy calculation that occurs after trajectory processing. + command will also MPI-parallelize the entropy calculation that occurs after + trajectory processing. \end_layout \begin_layout Standard @@ -1150,28 +1126,28 @@ The second is for 'ensemble' \series default \shape default - trajectory input, - where the reading/processing/writing of each member of the ensemble is divided up among MPI processes. + trajectory input, where the reading/processing/writing of each member of + the ensemble is divided up among MPI processes. The number of MPI processes must be a multiple of the ensemble size. - If the number of processes is greater than the ensemble size then the processing of each ensemble member will be divided among MPI processes (i.e. + If the number of processes is greater than the ensemble size then the processin +g of each ensemble member will be divided among MPI processes (i.e. across-trajectory parallelism will be used). - For example, - given an ensemble of 4 trajectories and 8 processes, - processes 0 and 1 are assigned to the first ensemble trajectory, - processes 2 and 3 are assigned to the second ensemble trajectory, - and so on. + For example, given an ensemble of 4 trajectories and 8 processes, processes + 0 and 1 are assigned to the first ensemble trajectory, processes 2 and + 3 are assigned to the second ensemble trajectory, and so on. When using ensemble mode in parallel it is recommended that the \series bold \emph on ensemblesize \series default \emph default - command be used prior to any ensemble command as this will make set up far more efficient. + command be used prior to any ensemble command as this will make set up + far more efficient. \end_layout \begin_layout Standard -Note that most Analyses are not MPI-parallelized, - with the exception of the +Note that most Analyses are not MPI-parallelized, with the exception of + the \series bold \emph on calcdiffusion @@ -1191,8 +1167,7 @@ noprefix "false" \end_layout \begin_layout Standard -In order to use the MPI version, - Amber/ +In order to use the MPI version, Amber/ \emph on cpptraj \emph default @@ -1201,9 +1176,8 @@ cpptraj \emph on cpptraj \emph default - has been compiled with MPI as it will print 'MPI' in the title, - and/or by calling 'cpptraj — -defines' and looking for '-DMPI'. + has been compiled with MPI as it will print 'MPI' in the title, and/or + by calling 'cpptraj —defines' and looking for '-DMPI'. \end_layout @@ -1223,7 +1197,8 @@ Some of the more time-consuming actions/analyses in \shape italic cpptraj \shape default - have been parallelized with OpenMP to take advantage of machines with multiple cores. + have been parallelized with OpenMP to take advantage of machines with multiple + cores. In order to use OpenMP parallelization Amber/ \emph on cpptraj @@ -1233,9 +1208,8 @@ cpptraj \shape italic cpptraj \shape default - has been compiled with OpenMP as it will print 'OpenMP' in the title, - and/or by calling 'cpptraj — -defines' and looking for '-D_OPENMP'. + has been compiled with OpenMP as it will print 'OpenMP' in the title, and/or + by calling 'cpptraj —defines' and looking for '-D_OPENMP'. The following actions/analyses have been OpenMP parallelized: \end_layout @@ -1357,7 +1331,8 @@ By default OpenMP cpptraj \shape default will use all available cores. - The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS environment variable. + The number of OpenMP threads can be controlled by setting the OMP_NUM_THREADS + environment variable. \end_layout \begin_layout Subsubsection @@ -1365,11 +1340,13 @@ CUDA Parallelization \end_layout \begin_layout Standard -Some time-consuming actions in cpptraj have been parallelized with CUDA to take advantage of machines with NVIDIA GPUs. - In order to use CUDA parallelization Amber/cpptraj should be configured with the '-cuda' flag. - You can easily tell if cpptraj has been compiled with CUDA as it will print 'CUDA' and details on the current graphics device in the title, - and/or by calling 'cpptraj — -defines' and looking for '-DCUDA'. +Some time-consuming actions in cpptraj have been parallelized with CUDA + to take advantage of machines with NVIDIA GPUs. + In order to use CUDA parallelization Amber/cpptraj should be configured + with the '-cuda' flag. + You can easily tell if cpptraj has been compiled with CUDA as it will print + 'CUDA' and details on the current graphics device in the title, and/or + by calling 'cpptraj —defines' and looking for '-DCUDA'. The following actions have been CUDA parallelized: \end_layout @@ -1399,8 +1376,8 @@ Units \begin_layout Standard Cpptraj uses the AKMA system of units. - The execption is time, - which is typically expressed in ps (except where noted). + The execption is time, which is typically expressed in ps (except where + noted). \begin_inset Separator latexpar \end_inset @@ -1579,17 +1556,16 @@ ptraj \family typewriter : \family default -', - ' +', ' \family typewriter @ \family default -', - and ' +', and ' \family typewriter * \family default -' are reserved for masks and should not be used in output file or data set names. +' are reserved for masks and should not be used in output file or data set + names. All masks are case-sensitive. Either names or numbers can be used. Masks can contain ranges (denoted with ' @@ -1601,13 +1577,11 @@ ptraj \family typewriter & \family default -' (and), - ' +' (and), ' \family typewriter | \family default -' (or), - and ' +' (or), and ' \family typewriter ! \family default @@ -1625,9 +1599,7 @@ The syntax for elementary selections is the following: \end_inset numlist} e.g. - '@12,17', - '@54-85', - '@12,54-85,90' + '@12,17', '@54-85', '@12,54-85,90' \end_layout \begin_layout Description @@ -1636,8 +1608,7 @@ numlist} e.g. \end_inset namelist} e.g. - '@CA', - '@CA,C,O,N,H' + '@CA', '@CA,C,O,N,H' \end_layout \begin_layout Description @@ -1664,9 +1635,7 @@ name} e.g. \end_inset numlist} e.g. - ':1-10', - ':1,3,5', - ':1-3,5,7-9' + ':1-10', ':1,3,5', ':1-3,5,7-9' \end_layout \begin_layout Description @@ -1675,8 +1644,7 @@ numlist} e.g. \end_inset namelist} e.g. - ':LYS', - ':ARG,ALA,GLY' + ':LYS', ':ARG,ALA,GLY' \end_layout \begin_layout Description @@ -1685,8 +1653,7 @@ namelist} e.g. \end_inset id} e.g. - '::B', - '::A,D'. + '::B', '::A,D'. Requires chain ID information be present in the topology. \end_layout @@ -1701,8 +1668,8 @@ residue number} e.g. ':;2-4,8'. - Requires a PDB loaded as topology, - or Amber topology with embedded PDB information (see + Requires a PDB loaded as topology, or Amber topology with embedded PDB + information (see \begin_inset CommandInset ref LatexCommand vref reference "subsec:parmed_addPDB" @@ -1718,8 +1685,7 @@ reference "subsec:parmed_addPDB" \end_inset numlist} e.g. - '^1-10', - ':23,84,111' + '^1-10', ':23,84,111' \end_layout \begin_layout Description @@ -1727,8 +1693,7 @@ numlist} e.g. \begin_inset space ~ \end_inset -operator> Selection by distance, - see below. +operator> Selection by distance, see below. \end_layout \begin_layout Standard @@ -1748,8 +1713,7 @@ Several wildcard characters are supported: \end_layout \begin_layout Standard -The wildcards can also be used with numbers or other mask characters, - e.g. +The wildcards can also be used with numbers or other mask characters, e.g. ':?0' means \begin_inset Quotes eld \end_inset @@ -1758,8 +1722,7 @@ The wildcards can also be used with numbers or other mask characters, \begin_inset Quotes erd \end_inset -, - ':*' means all residues and '@*' means all atoms. +, ':*' means all residues and '@*' means all atoms. If the atom name (or type name) contains a wildcard character like an asterisk, it can be explictly selected by escaping (i.e. preceding) the wildcard character with a backslash ' @@ -1773,11 +1736,7 @@ atoms @C?* \end_layout \begin_layout Standard -would select atoms named C5, - C4*, - C422, - etc., - but: +would select atoms named C5, C4*, C422, etc., but: \end_layout \begin_layout LyX-Code @@ -1799,8 +1758,7 @@ Compound expressions of the following type are allowed: \end_layout \begin_layout Standard -and are processed as: - +and are processed as: \end_layout \begin_layout LyX-Code @@ -1821,8 +1779,7 @@ e.g. \end_layout \begin_layout Standard -More examples: - +More examples: \end_layout \begin_layout Description @@ -1850,8 +1807,8 @@ More examples: \end_layout \begin_layout Description -:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not in water, - lysine or arginine residues. +:1-500@O&!(:WAT|:LYS,ARG) All backbone oxygens in residues 1-500 but not + in water, lysine or arginine residues. \end_layout \begin_layout Description @@ -1904,13 +1861,11 @@ operator> Distance operator. \end_layout \begin_layout Description -: - Any atom within a residue. +: Any atom within a residue. \end_layout \begin_layout Description -; - Residue geometric center. +; Residue geometric center. \end_layout \begin_layout Description @@ -1924,7 +1879,8 @@ operator> Distance operator. \end_deeper \begin_layout Standard -There are two very important things to keep in mind when using distance based masks: +There are two very important things to keep in mind when using distance + based masks: \end_layout \begin_layout Enumerate @@ -1954,8 +1910,7 @@ mask reference \series default \shape default -; - distances are then calculated using the +; distances are then calculated using the \bar under specified reference frame only \bar default @@ -1987,8 +1942,7 @@ The syntax for selection by distance is a \series bold \series default - consists of 2 characters: - ' + consists of 2 characters: ' \series bold < \series default @@ -2000,20 +1954,16 @@ The syntax for selection by distance is a \series bold ^ \series default -' (molecules), - ' +' (molecules), ' \series bold : \series default -' (residues), - ';' (residue centers), - or ' +' (residues), ';' (residue centers), or ' \series bold @ \series default ' (atoms). - For example, - ' + For example, ' \series bold <: \series default @@ -2026,16 +1976,15 @@ residues within 3.0 Angstroms \end_inset etc. - For ':' residue- and '^' molecule-based distance selection, - if any atom in that residue/molecule meets the given distance criterion, - the entire residue/molecule is selected. - For ';' residue center, - the geometric center of the residue must meet the given distance criterion in order to be selected. + For ':' residue- and '^' molecule-based distance selection, if any atom + in that residue/molecule meets the given distance criterion, the entire + residue/molecule is selected. + For ';' residue center, the geometric center of the residue must meet the + given distance criterion in order to be selected. \end_layout \begin_layout Standard -In plain language, - the entire distance mask can be read as +In plain language, the entire distance mask can be read as \begin_inset Quotes eld \end_inset @@ -2056,8 +2005,7 @@ Select \end_inset . - So for example, - the mask expression: + So for example, the mask expression: \end_layout \begin_layout LyX-Code @@ -2069,7 +2017,8 @@ Means \begin_inset Quotes eld \end_inset -Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues numbered 11 through 17) +Select atoms within 2.4 Å distance of atoms selected by ':11-17' (residues + numbered 11 through 17) \begin_inset Quotes erd \end_inset @@ -2100,19 +2049,15 @@ Ranges \begin_layout Standard For several commands some arguments are ranges (e.g. - 'trajout onlyframes ', - 'nastruct resrange ', - 'rmsd perres range '); - + 'trajout onlyframes ', 'nastruct resrange ', 'rmsd perres + range '); \series bold THESE ARE NOT ATOM MASKS \series default . - They are simple number ranges using '-' to specify a range and ',' to separate different ranges. - For example 1-2,4-6,9 specifies 1 to 2, - 4 to 6, - and 9, - i.e. + They are simple number ranges using '-' to specify a range and ',' to separate + different ranges. + For example 1-2,4-6,9 specifies 1 to 2, 4 to 6, and 9, i.e. '1 2 4 5 6 9'. \end_layout @@ -2129,16 +2074,16 @@ name "subsec:Parameter/Reference-Tagging" \begin_layout Standard Parameter and reference files may be 'tagged' (i.e. - given a nickname); - these tags can then be used in place of the file name itself. + given a nickname); these tags can then be used in place of the file name + itself. A tag in \shape italic cpptraj \shape default is recognized by being bounded by brackets ('[' and ']'). - This can be particularly useful when reading in many parameter or reference files. - For example, - when reading in multiple reference structures: + This can be particularly useful when reading in many parameter or reference + files. + For example, when reading in multiple reference structures: \end_layout \begin_layout LyX-Code @@ -2170,15 +2115,15 @@ rms Open ref [open] :2-12@CA out rmsd.dat \end_layout \begin_layout Standard -This defines three reference structures and gives them tags [xray], - [last], +This defines three reference structures and gives them tags [xray], [last], and [open]. - These reference structures can then be referred to by their tags instead of their filenames by any action that uses reference structures (in this case the RMSD action). + These reference structures can then be referred to by their tags instead + of their filenames by any action that uses reference structures (in this + case the RMSD action). \end_layout \begin_layout Standard -Similarly, - this can be useful when reading in multiple parameter files: +Similarly, this can be useful when reading in multiple parameter files: \end_layout \begin_layout LyX-Code @@ -2203,11 +2148,12 @@ rms ref [tz2] !(:WAT) out rmsd.dat \begin_layout Standard This defines two parm files and gives them tags [tz2-water] and [tz2-nowater], - then reads in a trajectory associated with one, - and a reference structure associated with the other. - Note that in the 'reference' command there are two tags; - the first goes along with the 'parm' keyword and specifies what parameter file the reference should use, - the second is the tag given to the reference itself (as in the previous example) and is referred to in the subsequent RMSD action. + then reads in a trajectory associated with one, and a reference structure + associated with the other. + Note that in the 'reference' command there are two tags; the first goes + along with the 'parm' keyword and specifies what parameter file the reference + should use, the second is the tag given to the reference itself (as in + the previous example) and is referred to in the subsequent RMSD action. \end_layout \begin_layout Section @@ -2215,8 +2161,7 @@ Variables and Control Structures \end_layout \begin_layout Standard -As of version 18, - CPPTRAJ has limited support for +As of version 18, CPPTRAJ has limited support for \begin_inset Quotes eld \end_inset @@ -2225,8 +2170,10 @@ script \end_inset variables and 'for' loops. - Script variables are referred to by a dollar sign ('$') prefix and are replaced when they are processed. - These are stored in the master data set list like other data and are assigned the type + Script variables are referred to by a dollar sign ('$') prefix and are + replaced when they are processed. + These are stored in the master data set list like other data and are assigned + the type \begin_inset Quotes eld \end_inset @@ -2237,12 +2184,11 @@ string variable . \series bold -Note that to use script variables in CPPTRAJ input that is inside another script (e.g. - a BASH script), - they must be escaped with the ' +Note that to use script variables in CPPTRAJ input that is inside another + script (e.g. + a BASH script), they must be escaped with the ' \backslash ' character, - \series default e.g. \end_layout @@ -2274,7 +2220,9 @@ EOF \end_layout \begin_layout Standard -Note that regular CPPTRAJ 1D Data Sets that contain a single value can be used as script variables (if the Data Set contains more than 1 value only the first value will be used). +Note that regular CPPTRAJ 1D Data Sets that contain a single value can be + used as script variables (if the Data Set contains more than 1 value only + the first value will be used). \end_layout \begin_layout Standard @@ -2412,21 +2360,15 @@ for { {atoms|residues|molecules|molfirstres|mollastres} \end_layout \begin_layout LyX-Code - END KEYWORD: - 'done' + END KEYWORD: 'done' \end_layout \begin_layout LyX-Code - Available 'end OP' : - '<' '>' '<=' '>=' + Available 'end OP' : '<' '>' '<=' '>=' \end_layout \begin_layout LyX-Code - Available 'increment OP' : - '++', - '--', - '+=', - '-=' + Available 'increment OP' : '++', '--', '+=', '-=' \end_layout \begin_deeper @@ -2443,8 +2385,9 @@ inmask \begin_inset space ~ \end_inset - Loop over atoms/residues/molecules/first residue in molecules/last residue in molecules selected by the given mask expression, - set as script variable + Loop over atoms/residues/molecules/first residue in molecules/last + residue in molecules selected by the given mask expression, set as script + variable \series bold \series default @@ -2558,8 +2501,8 @@ blocksize \end_layout \begin_layout Description -[cumulative] Instead of blocks of fixed size, - use blocks of increasing size incremented by blocksize. +[cumulative] Instead of blocks of fixed size, use blocks of increasing size + incremented by blocksize. \end_layout \begin_deeper @@ -2568,8 +2511,8 @@ blocksize \begin_inset space ~ \end_inset -<#>] When cumulative, - the size of the first block (default is first data set element). +<#>] When cumulative, the size of the first block (default is first data + set element). \end_layout \end_deeper @@ -2591,13 +2534,11 @@ OP>[] Loop over integer script variable \series bold \series default -, - optionally ending at +, optionally ending at \series bold \series default -, - increment by +, increment by \series bold \series default @@ -2613,7 +2554,8 @@ Data Sets Created (datasetblocks loops): \begin_inset space \space{} \end_inset -idx> (Data set blocks only) Data set block of blocksize starting at . +idx> (Data set blocks only) Data set block of blocksize starting at . \end_layout \begin_layout Description @@ -2621,17 +2563,17 @@ idx> (Data set blocks only) Data set block of blocksize starting at . \begin_inset space ~ \end_inset -idx> (Cumulative data set blocks only) Data set block starting at firstblock and ending at . +idx> (Cumulative data set blocks only) Data set block starting at firstblock + and ending at . \end_layout \end_deeper \begin_layout Standard -Create a for loop using one or more mask expressions, - integers, - etc. +Create a for loop using one or more mask expressions, integers, etc. Loops can be nested inside each other. - Integer loops may be used without an end condition, - but in that case at least one descriptor in the loop should have an end condition or refer to a mask. + Integer loops may be used without an end condition, but in that case at + least one descriptor in the loop should have an end condition or refer + to a mask. Loops are ended by the \series bold done @@ -2642,8 +2584,7 @@ done \begin_layout Standard Note that non-integer variables (e.g. - 'inmask' loops) are NOT incremented after the final loop iteration, - i.e. + 'inmask' loops) are NOT incremented after the final loop iteration, i.e. these loop variables always retain their final value. \end_layout @@ -2664,9 +2605,10 @@ done \end_layout \begin_layout Standard -This loops over all atoms in the mask expression ':1-3@CA' (all atoms named CA in residues 1 to 3) and creates a variable named 'i' that starts from 1 and is incremented by 1 each iteration. - Inside the loop, - the mask selection is referred to by +This loops over all atoms in the mask expression ':1-3@CA' (all atoms named + CA in residues 1 to 3) and creates a variable named 'i' that starts from + 1 and is incremented by 1 each iteration. + Inside the loop, the mask selection is referred to by \series bold $A0 \series default @@ -2735,9 +2677,7 @@ set { | \end_layout \begin_layout LyX-Code - Available : - '=', - '+=' + Available : '=', '+=' \end_layout \begin_deeper @@ -2774,9 +2714,10 @@ inmask \begin_inset space ~ \end_inset - Set/append a script variable to/by the total number of atoms/residues/molecules in, - a range expression of selected atom #s/residue #s/original residue #s/molecule #s in, - or the total charge/mass of atoms selected by the given mask expression. + Set/append a script variable to/by the total number of atoms/residues/mol +ecules in, a range expression of selected atom #s/residue #s/original residue + #s/molecule #s in, or the total charge/mass of atoms selected by the given + mask expression. \end_layout \begin_deeper @@ -2818,7 +2759,8 @@ parmindex \begin_inset space ~ \end_inset -trajinframes Set/append a script variable to/by the total number of frames in trajectories currently loaded by +trajinframes Set/append a script variable to/by the total number of frames + in trajectories currently loaded by \series bold \emph on trajin @@ -2830,13 +2772,12 @@ trajin \end_deeper \begin_layout Standard Set ( = '=') or append ( = '+=') a script variable. - Script variables are character strings, - and are referred to in CPPTRAJ input by using a dollar sign '$' prefix. + Script variables are character strings, and are referred to in CPPTRAJ + input by using a dollar sign '$' prefix. \end_layout \begin_layout Standard -For example, - the following input will load files my.parm7 and my.rst7: +For example, the following input will load files my.parm7 and my.rst7: \end_layout \begin_layout LyX-Code @@ -2852,8 +2793,8 @@ trajin $PREFIX.rst7 \end_layout \begin_layout Standard -For example, - the following input will print info for the last 10 atoms in a topology to 'last10.dat': +For example, the following input will print info for the last 10 atoms in + a topology to 'last10.dat': \end_layout \begin_layout LyX-Code @@ -2881,8 +2822,7 @@ The following input will put a range of residues selected by :LYS: \end_layout \begin_layout LyX-Code - Using topology: - FtuFabI.NAD.TCL.parm7 + Using topology: FtuFabI.NAD.TCL.parm7 \end_layout \begin_layout LyX-Code @@ -2898,10 +2838,9 @@ show [ ...] \end_layout \begin_layout Standard -If no variable names specified, - show all current script variables and their values. - Otherwise, - show the values of the specified script variables. +If no variable names specified, show all current script variables and their + values. + Otherwise, show the values of the specified script variables. \end_layout \begin_layout Section @@ -2913,19 +2852,19 @@ In \shape italic cpptraj \shape default -, - Actions and Analyses can generate one or more data sets which are available for further processing. - For example, - the +, Actions and Analyses can generate one or more data sets which are available + for further processing. + For example, the \series bold \shape italic distance \series default \shape default command creates a data set containing distances vs time. - The data set can be named by the user simply by specifying a non-keyword string as an additional argument. - If no name is given, - a default one will be generated based on the action name and data set number. + The data set can be named by the user simply by specifying a non-keyword + string as an additional argument. + If no name is given, a default one will be generated based on the action + name and data set number. For example: \end_layout @@ -2943,8 +2882,7 @@ d1-2 \end_inset . - If a name is not specified, - e.g.: + If a name is not specified, e.g.: \end_layout \begin_layout LyX-Code @@ -2964,8 +2902,7 @@ Dis_00000 \end_layout \begin_layout Standard -Data files are created automatically by most commands, - usually via the +Data files are created automatically by most commands, usually via the \begin_inset Quotes eld \end_inset @@ -3009,29 +2946,27 @@ reference "tab:cpptraj-DataFile-formats" \end_inset -, - although it cannot write in all formats. - In addition, - a data set must be valid for the data file format. - For example, - 3D data (such as a grid) can be written to an OpenDX format file but not a Grace format file. +, although it cannot write in all formats. + In addition, a data set must be valid for the data file format. + For example, 3D data (such as a grid) can be written to an OpenDX format + file but not a Grace format file. \end_layout \begin_layout Standard -The default file format is called 'Standard', - which simply has data in columns, +The default file format is called 'Standard', which simply has data in columns, like \shape italic ptraj \shape default -, - although multiple data sets can be directed to the same output file. - The format of a file can be changed either by specifying a recognized keyword (either on the command line itself or later via a 'datafile' command) or by giving the file an extension corresponding to te format, - so 'filename.agr' will output in Grace format, - and 'filename.gnu' will output in Gnuplot contour, +, although multiple data sets can be directed to the same output file. + The format of a file can be changed either by specifying a recognized keyword + (either on the command line itself or later via a 'datafile' command) or + by giving the file an extension corresponding to te format, so 'filename.agr' + will output in Grace format, and 'filename.gnu' will output in Gnuplot contour, and so on. - The xmgrace/gnuplot output is particularly nice for the secstruct sumout and rmsd perresout files. + The xmgrace/gnuplot output is particularly nice for the secstruct sumout + and rmsd perresout files. Additional options for data files can be found in \begin_inset CommandInset ref LatexCommand vref @@ -3051,9 +2986,9 @@ out \begin_inset Quotes erd \end_inset - keyword will allow data sets from separate commands to be written into the same file. - For example, - the commands: + keyword will allow data sets from separate commands to be written into + the same file. + For example, the commands: \end_layout \begin_layout LyX-Code @@ -3097,8 +3032,8 @@ phipsi.dat \end_layout \begin_layout Standard -Note that when reading the Amber Prep and Amber OFF Library formats, - a COORDS data set will be created for each unit present in these files. +Note that when reading the Amber Prep and Amber OFF Library formats, a COORDS + data set will be created for each unit present in these files. \end_layout \begin_layout Standard @@ -3206,9 +3141,7 @@ dat \begin_inset Text \begin_layout Plain Layout -1D, - 2D, - 3D +1D, 2D, 3D \end_layout \end_inset @@ -3237,8 +3170,7 @@ Grace \begin_inset Text \begin_layout Plain Layout -.agr, - .xmgr +.agr, .xmgr \end_layout \end_inset @@ -3303,8 +3235,7 @@ gnu \begin_inset Text \begin_layout Plain Layout -1D, - 2D +1D, 2D \end_layout \end_inset @@ -3333,8 +3264,7 @@ Xplor \begin_inset Text \begin_layout Plain Layout -.xplor, - .grid +.xplor, .grid \end_layout \end_inset @@ -3502,8 +3432,7 @@ mdout \begin_inset Text \begin_layout Plain Layout -Energy information, - Read Only +Energy information, Read Only \end_layout \end_inset @@ -3926,8 +3855,7 @@ charmmout \begin_inset Text \begin_layout Plain Layout -Energy information, - Read Only +Energy information, Read Only \end_layout \end_inset @@ -4135,8 +4063,7 @@ Amber OFF Library File \begin_inset Text \begin_layout Plain Layout -.off, - .lib +.off, .lib \end_layout \end_inset @@ -4230,10 +4157,8 @@ entire \series bold : - \series default - The data set name, - usually specified in the action (e.g. + The data set name, usually specified in the action (e.g. in 'distance d0 @1 @2' the data set name is \begin_inset Quotes eld \end_inset @@ -4249,18 +4174,16 @@ d0 \series bold : - \series default - Optional; - this is set for certain data sets internally in order to easily select subsets of data. + Optional; this is set for certain data sets internally in order to easily + select subsets of data. \series bold The brackets are required \series default . - For example, - when using 'hbond series', - both solute-solute and solute-solvent hydrogen bond time series may be generated. + For example, when using 'hbond series', both solute-solute and solute-solvent + hydrogen bond time series may be generated. To select all solute-solute hydrogen bonds one would use the aspect \begin_inset Quotes eld \end_inset @@ -4269,8 +4192,7 @@ The brackets are required \begin_inset Quotes erd \end_inset -; - to select solute-solvent hydrogen bonds the aspect +; to select solute-solvent hydrogen bonds the aspect \begin_inset Quotes eld \end_inset @@ -4286,20 +4208,16 @@ The brackets are required \series bold : - \series default - Optional; - for actions that generate many data sets (such as 'rmsd perres') an index is used. - Depending on the action, - the index may correspond to atom #s, - residue #s, + Optional; for actions that generate many data sets (such as 'rmsd perres') + an index is used. + Depending on the action, the index may correspond to atom #s, residue #s, etc. A number range (comma and/or dash separated) may be used. \end_layout \begin_layout Standard -For example: - to select all data sets with aspect +For example: to select all data sets with aspect \begin_inset Quotes eld \end_inset @@ -4323,8 +4241,7 @@ To select all data sets with aspect \begin_inset Quotes erd \end_inset - with any name, - indices 1 and 3: + with any name, indices 1 and 3: \end_layout \begin_layout LyX-Code @@ -4332,8 +4249,7 @@ To select all data sets with aspect \end_layout \begin_layout Standard -In ensemble mode, - data set selection has additional syntax: +In ensemble mode, data set selection has additional syntax: \end_layout \begin_layout LyX-Code @@ -4356,13 +4272,11 @@ name "subsec:cpptraj-Data-Set-Math" \end_layout \begin_layout Standard -As of version 15, - +As of version 15, \emph on cpptraj \emph default - can perform basic math operations, - even on data sets (with some limitations). + can perform basic math operations, even on data sets (with some limitations). Currently recognized operations are: \begin_inset Separator latexpar \end_inset @@ -4843,13 +4757,11 @@ E \begin_inset Quotes erd \end_inset - notation, - e.g. + notation, e.g. 1E-5 = 0.00001. The parser also recognizes PI as the number pi. Expressions can also be enclosed in parentheses. - So for example, - the following expression is valid: + So for example, the following expression is valid: \end_layout \begin_layout LyX-Code @@ -4857,12 +4769,12 @@ E \end_layout \begin_layout LyX-Code -Result: - 0.879887 +Result: 0.879887 \end_layout \begin_layout Standard -Results of numerical calculations like the above can be assigned to a variable (essentially a data set of size 1) for use in subsequent calculations, +Results of numerical calculations like the above can be assigned to a variable + (essentially a data set of size 1) for use in subsequent calculations, e.g. \end_layout @@ -4875,18 +4787,15 @@ Result stored in 'R' \end_layout \begin_layout LyX-Code -> R + 1 Result: - 1.879887 +> R + 1 Result: 1.879887 \end_layout \begin_layout Standard Data sets can be specified in expressions as well. - Currently data sets in an expression must be of the same type and only 1D, - 2D, - and 3D data sets are supported. + Currently data sets in an expression must be of the same type and only + 1D, 2D, and 3D data sets are supported. Functions are applied to each member of the data set. - So for example, - given two 1D data sets of the same size named D0 and D1, + So for example, given two 1D data sets of the same size named D0 and D1, the following expression: \end_layout @@ -4895,9 +4804,8 @@ Data sets can be specified in expressions as well. \end_layout \begin_layout Standard -would take the square root of each member of D0, - add it to the corresponding member of D1, - and assign the result to D2. +would take the square root of each member of D0, add it to the corresponding + member of D1, and assign the result to D2. The following table lists which operations are valid for data set types. If a type is not listed it is not supported: \begin_inset Separator latexpar @@ -4966,9 +4874,7 @@ Notes \begin_inset Text \begin_layout Plain Layout -1D (integer, - double, - float) +1D (integer, double, float) \end_layout \end_inset @@ -5015,11 +4921,7 @@ All \begin_inset Text \begin_layout Plain Layout -+, - -, - *, - /, - = ++, -, *, /, = \end_layout \end_inset @@ -5057,11 +4959,7 @@ None \begin_inset Text \begin_layout Plain Layout -+, - -, - /, - *, - = ++, -, /, *, = \end_layout \end_inset @@ -5070,11 +4968,7 @@ None \begin_inset Text \begin_layout Plain Layout -sum, - avg, - stdev, - min, - max +sum, avg, stdev, min, max \end_layout \end_inset @@ -5103,11 +4997,7 @@ sum, \begin_inset Text \begin_layout Plain Layout -+, - -, - /, - *, - = ++, -, /, *, = \end_layout \end_inset @@ -5116,11 +5006,7 @@ sum, \begin_inset Text \begin_layout Plain Layout -sum, - avg, - stdev, - min, - max +sum, avg, stdev, min, max \end_layout \end_inset @@ -5155,8 +5041,8 @@ name "sec:Datafile-Commands" \begin_layout Standard Data file output can be handled multiple ways in cpptraj. - Output data files can be created by Actions/Analyses/Commands, - or can be explicitly created with + Output data files can be created by Actions/Analyses/Commands, or can be + explicitly created with \series bold \emph on writedata @@ -5200,14 +5086,12 @@ reference "subsec:cpptraj_readdata" \end_layout \begin_layout Standard -In general, - data files which have been declared with an +In general, data files which have been declared with an \series bold 'out' \series default keyword will recognize data file write keywords on the same command line. - For example, - the + For example, the \series bold 'time' \series default @@ -5225,8 +5109,10 @@ distance d0 :1 :2 out d0.agr time 0.001 \end_layout \begin_layout Standard -The data file format can be changed from standard implicitly by using specific filename extensions or keywords. - If the extension is not recognized or no keyword is give the default format is 'Standard'. +The data file format can be changed from standard implicitly by using specific + filename extensions or keywords. + If the extension is not recognized or no keyword is give the default format + is 'Standard'. Keywords and extensions for data file formats recognized by \shape italic cpptraj @@ -5239,7 +5125,8 @@ reference "tab:cpptraj-DataFile-formats" \end_inset . - Note that the use of certain options may be restricted for certain data file formats. + Note that the use of certain options may be restricted for certain data + file formats. These options can also be passed to data files via the \series bold \emph on @@ -5300,7 +5187,8 @@ zlabel}