Tools and information for AMBER and CPPTRAJ examples
Updated: May 31, 2022
Read data files in ensemble mode. readensembledata <filename> [filenames <additional files>] [<readdata args>] <lename> Lowest replica file name. filenames <additional files> Specified additional members of the ensemble. If not specified ensemble members will be search for using numerical… Read More
Category: CPPTRAJ, Trajectory File Commands
Updated: December 1, 2022
Set up an output trajectory or ensemble for writing during a Run. trajout <filename> [<format>] [append] [nobox] [novelocity] [notemperature] [notime] [noforce] [noreplicadim] [parm <parmfile> | parmindex <#>] [onlyframes <range>] [title <title>] [onlymembers <memberlist>] [start <start>] [stop <stop>] [offset… 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: March 21, 2019
Set up a trajectory for reading during a Run. trajin <filename> {[<start> [<stop> | last] [<offset>]]} | lastframe [parm <parmfile / tag> | parmindex <#>] [mdvel <velocities>] [mdfrc <forces>] [ <Format Options> ] [ remdtraj {remdtrajtemp <Temperature> |… Read More
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