Tools and information for AMBER and CPPTRAJ examples
Updated: October 10, 2023
Print total charge for selected atoms. charge [parm <name> | parmindex <#> | <#>] <mask> [out <file>] [name <set>] parm <name> | parmindex <#> Topology to calculate charge from. <mask> Atom(s) to calculate total charge for (default all)…. Read More
Updated: March 27, 2019
Print bond info for selected atoms bondinfo [parm <name> | parmindex <#> | <#>] [<mask>] Print bond information for atoms in <mask> for selected topology (first loaded topology by default) with format: # Bond Kb Req atom names … Read More
Updated: March 27, 2019
Print details for selected atoms atominfo [parm <name> | parmindex <#> | <#>] [<mask>] Print information on atoms in <mask> for selected topology (first loaded topology by default) with format: #Atom Name #Res Name #Mol Type Charge Mass… Read More
Updated: March 27, 2019
Print angle info for selected atoms angleinfo [parm <name> | parmindex <#> | <#>] [<mask>] Print angle information of atoms in <mask> for selected topology (first loaded topology by default) with format: # Angle Kthet degrees atom names… Read More
Updated: November 20, 2024
Set up an output trajectory or ensemble for writing during a Run. trajout <filename> [<format>] [append] [nobox] [novelocity] [notemperature] [notime] … Read More
Updated: March 27, 2019
Load a single trajectory frame as a reference. reference <name> [<frame#>] [<mask>] ([tag]) [lastframe] [crdset][parm <parmfile / tag> | parmindex <#>] <name> File name (or COORDS set name if ’crdset’ specified) to read in as reference; any trajectory… Read More
Updated: March 21, 2019
Specify number of members expected in subsequent ensemble commands. ensemblesize <#> This command is MPI only. It is used to set the expected number of members in any subsequent ensemble command, which dramatically improves set up efficiency.
Updated: March 21, 2019
Set up a trajectory ensemble for reading during a run. ensemble <file0> {[<start>] [<stop> | last] [offset]} | lastframe [parm <parmfile / tag> | parmindex <#>] [trajnames <file1>,<file2>,…,<fileN> [remlog <remlogfile> [nstlim <nstlim> ntwx <ntwx>]] <file0> Lowest replica filename…. Read More
Updated: November 1, 2022
Calculate radial distribution function. radial [out <outfilename>] <spacing> <maximum> <solvent mask1> [<solute mask2>] [noimage] [density <density> | volume] [<dataset name>][intrdf <file>] [rawrdf <file>] [{{center1|center2|nointramol} | [byres1] [byres2] [bymol1] [bymol2]}]] out <outfilename> File to write RDF to, required. <spacing>… Read More
Updated: March 25, 2019
Calculate the number of waters in the first and second solvation shells based on distance critera. watershell <solutemask> [out <filename>] [lower <lower cut>] [upper <upper cut>] [noimage] [<solventmask>] <solutemask> Atom mask corresponding to solute of interest (required). [out… Read More
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