Tools and information for AMBER and CPPTRAJ examples
Updated: September 17, 2025
Calculate radial distribution function. radial [out <outfilename>] <spacing> <maximum> <solvent mask1> [<solute mask2>] [noimage] [mass] [density <density> | volume] [<dataset name>] [intrdf <file>] [rawrdf <file>] [{{center1|center2|nointramol|toxyz <x>,<y>,<z>} | … 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
Updated: March 25, 2019
Calculate unit cell volume. volume [<name>] [out <filename>] <name> Data set name. out <filename> Output file name.
Updated: March 25, 2019
Create volumetric map for specified coordinates; similar to grid but takes into account atomic radii. Similar to VMD volmap. volmap filename dx dy dz <mask> [radscale <factor>] { data <existing set> | name <setname> { size <x,y,z> [center… Read More
Updated: March 25, 2019
Calculate velocity autocorrelation function. velocityautocorr [<set name>] [<mask>] [usevelocity] [out <filename>] [diffout <file>] [maxlag <frames>] [tstep <timestep>] [direct] [norm] [<set name>] Data set name. [<mask>] Atoms(s) to calculate velocity autocorrelation (VAC) function for. [usevelocity] Use velocity information in… Read More
Updated: November 20, 2024
Calculate various types of vector quantities. vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>] [magnitude] [geom] [ired] [gridset <grid>] [debye] <Type> = { mask | minimage | dipole | center | corrplane | box | boxcenter | ucellx… Read More
Updated: May 12, 2023
Reverse of image; unwrap selected atoms so they have continuous trajectories. unwrap [center] [{bymol | byres | byatom}] [ reference | ref <name> | refindex <#> ] [<mask>] [center]… Read More
Updated: March 25, 2019
Undo all previous strip Action commands. Requests that the original topology and frame be used for all following actions. This has the effect of undoing any command that modifies the state (such as strip). For example, the following… Read More
Updated: March 25, 2019
Translate specified atoms by specified amounts in X/Y/Z directions. translate [<mask>] [x <dx>] [y <dy>] [z <dz>] Translate atoms in <mask> (all atoms if no mask specified) <dx> Å in the X direction, <dy> Å in the Y… Read More
Updated: September 29, 2023
Calculate system temperature using velocities of specified atoms. temperature [<name>] [out <filename>] {frame | [<mask>] [ntc <#>] [update] [remove {trans|rot|both}] … Read More
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