Category: Action Commands

avgbox

Calculate average unit cell (box), primarily for unwrapping NPT trajectories. avgbox [name ] [out ] [name ] Average unit cell data set name.        [out <file>] File to write average unit cell data to. DataSets created:… Read More

lipidscd

Calculate lipid order parameters SCD(|<P2>|) for lipid chains. Automatically identifies lipids. lipidscd [<name>] [<mask>] [{x|y|z}] [out <file>] [p2] <name> Output data set name. <mask> Atom mask specifying where to search for lipids. x|y|z Axis to calculate order parameters… Read More

remap

Re-map atoms according to a given data set. remap data <setname> [outprefix <prefix>]                      [nobox]                      [parmout <filename>]    … Read More

time

Add/remove/modify time information in frames. time {time0 <initial time> dt <step> [update] | remove} time0 <initial time> Time of the first frame (ps). dt <step> Time step between frames (ps). [update] If specified, modify any existing time info…. Read More

xtalsymm

Re-image coordinates based on crystal space group symmetry operations and asymmetric unit volume. xtalsymm <mask> group <space group> [collect [centroid]] [ first | reference | ref <name> | refindex <#> ] [na <na>] [nb <nb>] [nc <nc>] <mask>… Read More

fiximagedbonds

Fix bonds which have been split across periodic boundaries by imaging. fiximagedbonds [<mask>] <mask> Mask expression of atoms to check. Fix bonds that have been split across periodic boundary conditions by imaging. It may be desirable to reimage… Read More

dihrms

Calculate the RMSD of dihedrals to dihedrals in a reference structure. dihedralrms [<name>] <dihedral types> [out <file>] [ first | reference | ref <name> | refindex <#> | previous | reftraj <name> [parm <name> | parmindex <#>] ]… Read More

keep

Keep specified atoms in system. keep [ bridgedata <bridge data set>      [nbridge <#>]      [nobridgewarn]      [bridgeresname <res name>] bridgeresonly <resrange>] ]      [keepmask <atoms to keep>]      [charge <new charge>]  … Read More