matrix
matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>] [name <name>] [ byatom | byres [mass] | bymask [mass] ] [ ired [order <#>] ] [ {distcovar | idea} <mask1> ] [ {dist | correl | covar |… Read More
Tools and information for AMBER and CPPTRAJ examples
Posted: February 21, 2019
matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>] [name <name>] [ byatom | byres [mass] | bymask [mass] ] [ ired [order <#>] ] [ {distcovar | idea} <mask1> ] [ {dist | correl | covar |… Read More
Updated: March 27, 2019
List various objects in the CPPTRAJ state list <type> (<type> = actions,trajin,trajout,ref,parm,analysis,datafile,dataset) List the currently loaded objects of <type>.
Updated: March 27, 2019
Run an analysis immediately or run all queued analyses runanalysis [<analysiscmd> [<analysis args>]] Run given analysis command immediately and write any data generated. If no command is given run any analysis currently set up. NOTE: When ’runanalysis’ is… Read More
Updated: March 28, 2019
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. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’)…. Read More
Updated: August 30, 2023
cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>][-ya <args>] [-xa <args>] [<file>] [-c <reference>] [-d <datain>] [-w <dataout>] [-o <output>] [-h | –help] [-V | –version] [–defines] [-debug <#>] [–interactive] [–log <logfile>] [-tl] [-ms <mask>] [-mr <mask>]… Read More
Updated: April 12, 2023
Calculate hydrogen bonds using geometric criteria. hbond [<dsname>] [out <filename>] [<mask>] [angle <acut>] [dist <dcut>] [donormask <dmask> [donorhmask <dhmask>]] [acceptormask… Read More
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