Tag: action commands

radial | rdf

Calculate radial distribution function. radial <outfilename> <spacing> <maximum> <solvent mask1>[<solute mask2>] [noimage] [density <density> | volume][center1 | center2 | nointramol] [<name>][intrdf <file>] [rawrdf <file>] <outfilename> File to write RDF to, required. <spacing> Bin spacing, required. <maximum> Max bin… Read More

watershell

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

volmap

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

velocityautocorr

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

vector

Calculate various types of vector quantities. vector [<name>] <Type> [out <filename> [ptrajoutput]] [<mask1>] [<mask2>] [magnitude] [ired] <Type> = { mask | minimage | dipole | center | corrplane | box | boxcenter | ucellx | ucelly | ucellz… Read More

unwrap

Reverse of image; unwrap selected atoms so they have continuous trajectories. unwrap [center] [{bymol | byres | byatom}] [ reference | ref <name> | refindex <#> ] [<mask>] [center] Unwrap by center of mass; otherwise unwrap by first… Read More

unstrip

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

temperature

Calculate system temperature using velocities of specified atoms. temperature [<name>] {frame | [<mask>] [ntc <#>]} [out <filename>] [<name>] Data set name. frame Do not calculate temperature; use existing frame temperature. [<mask>] Atoms to calculate temperature for. [ntc <#>]… Read More