Tools and information for AMBER and CPPTRAJ examples
Updated: March 27, 2019
Select the reference for distance-based masks activeref <#> Set which reference structure should be used when setting up distance-based masks for everything but the mask action. Numbering starts from 0, so ’activeref 0’ selects the first reference structure… Read More
Updated: March 27, 2019
Clear various objects from the CPPTRAJ state clear [{all | <type>}] <type> = actions, trajin, trajout, ref, parm, analysis, datafile, dataset Clear list of indicated type, or all lists if ’all’ specified. Note that when clearing actions or… Read More
Updated: April 11, 2023
Create (but do not yet write) a data file create <filename> <datasetname0> [<datasetname1> …] [<DataFile Options>] Add specified data sets to the data file named <filename>; if the file does not exist, it will be added to the… Read More
Updated: May 31, 2019
Used to manipulate data files datafile <filename> <datafile arg> Used to manipulate data files. Pass <datafile arg> to data file <filename>. See Data Files Options for more details.
Updated: March 27, 2019
Filter data sets based on given criteria datafilter <dataset arg> min <min> max <max> [out <file> [name <setname>]] <dataset arg> min <min> max <max> Data set and min/max cutoffs to use; can specify more than once. [out <file>]… Read More
Updated: November 18, 2023
Use to manipulate data sets dataset { legend <legend> <set> | makexy <Xset> <Yset> [name <name>] | vectorcoord {X|Y|Z} <set> [name <name>] | cat <set0> <set1> … [name <name>] [nooffset] | make2d <1D set>… Read More
Updated: April 5, 2022
Set debug level. Higher levels give more info debug [<type>] <#> <type> = actions, trajin, trajout, ref, parm, analysis, datafile, dataset Set the level of debug information to print. In general the higher the <#> the more information… Read More
Posted: February 25, 2019
Exit normally.
Updated: March 20, 2019
Begin trajectory processing, followed by analysis and datafile write.
Updated: March 27, 2019
Provide help for commands help {[<command>] | General | Action | Analysis | Topology | Trajectory} By itself, list all commands known to CPPTRAJ. If given with a command, print help for that command. Otherwise, list all commands… Read More
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