emin
Run simple energy minimization on a frame of a COORDS set. emin crdset <name> [trajoutname <name>] [rmstol <tol>] [nsteps <#>] [<mask>] [frame <#>] [dx0 <step0>] [out… Read More
Tools and information for AMBER and CPPTRAJ examples
Updated: June 30, 2023
Run simple energy minimization on a frame of a COORDS set. emin crdset <name> [trajoutname <name>] [rmstol <tol>] [nsteps <#>] [<mask>] [frame <#>] [dx0 <step0>] [out… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Posted: April 5, 2022
Concatenate two or more COORDS sets. catcrd <crd1> <crd2> … name <name> <crdX> COORDS data sets to concatenate, specify 2 or more. name <name> New COORDS set name. Concatenate two or more COORDS data sets into a single… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: May 18, 2023
Graft part of one COORDS set onto another COORDS set graft src <source COORDS> [srcframe <#>] [srcfitmask <mask>] … Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: August 31, 2023
Combine two or more COORDS sets combinecrd <crd1> <crd2> … [parmname <topname>] [crdname <crdname>] <crdX> COORDS data set to combine, specify 2 or more. [parmname <topname>] Name of combined Topology. [crdname <crdname>] Name of combined COORDS data set…. Read More
Updated: February 26, 2020
Run a single Action on a COORDS set. crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offset>] Perform action <actioncmd> on COORDS data set <crd set>. A subset of frames in the COORDS data set can be specified with… Read More
Updated: April 5, 2022
Write a COORDS set to a file crdout <crd set> <filename> [<trajout args>] [crdframes <start>,<stop>,<offset>] Write COORDS data set <crd set> to trajectory named <filename>. A subset of frames in the COORDS data set can be specified with… Read More
Updated: March 27, 2019
Create a COORDS set during a run This command is actually an Action that can be used to create COORDS data sets during trajectory processing, see the createcrd command.
Updated: December 1, 2022
Create or append to a COORDS set from a file loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>] [prec {single|double} <filename> Trajectory file to load. [parm <parmle/tag>] Topology filename/tag to associate with trajectory (default first topology)…. Read More
Updated: April 5, 2022
Create special COORDS set where frames remain on disk loadtraj name <setname> [<filename>] This command functions in two ways. If <filename> is not provided, all currently loaded input trajectories (from trajin commands) are added to TRAJ data set… Read More
Updated: March 27, 2019
Rotate specified dihedral(s) in given COORDS set by specific interval or to random values permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}] [outtraj <filename> [<outfmt>]] [crdout <output COORDS>] [<dihedral types>] Options for ’random’: [rseed <rseed>] [out <#… Read More
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