Category: Action Commands

mindist/maxdist

Posted: November 20, 2024

Calculate the minimum or maximum distance between pairs of atoms/residues/molecules {min|max}dist mask1 <mask1> [mask2 <mask2>] [{byatom|byres|bymol}] [noimage] [name <setname>] [out <file>] [resoffset <#>] mask1 <mask1> First mask for selecting atoms. [mask2 <mask2>] Optional second mask for selecting atoms…. Read More

Category: Action Commands, CPPTRAJ

enedecomp

Updated: November 20, 2024

enedecomp Perform per-atom energy decomposition. enedecomp [<name>] [<mask>] [out <filename>] [ pme [cut <cutoff>] [dsumtol <dtol>] [ewcoeff <coeff>] [erfcdx <dx>] [skinnb <skinnb>] [ljswidth <width>] [order <order>] [nfft <nfft1>,<nfft2>,<nfft3>] [<name>] Data set name. [<mask>] Mask of atoms to calculate… Read More

Category: Action Commands, CPPTRAJ

addatom

Posted: July 12, 2024

addatom – aname <name> [elt <element>] [rname <res name>] [xyz <X> <Y> <Z>] [mass <mass>] [charge <charge>] [outprefix <prefix>] [nobox] [parmout <filename>] [parmopts <comma-separated-list>] This is mostly useful for adding a placeholder “dummy” atom for subsequent actions to… Read More

Category: Action Commands, CPPTRAJ

multipucker

Updated: January 12, 2024

Calculate specified pucker types for residues in given range. multipucker [<name>] [<pucker types>] [out <filename>] [resrange <range>] … Read More

Category: Action Commands, CPPTRAJ

avgbox

Posted: May 30, 2023

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

Category: Action Commands, CPPTRAJ

lipidscd

Updated: April 10, 2022

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

Category: Action Commands, CPPTRAJ

remap

Updated: November 28, 2023

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

Category: Action Commands, CPPTRAJ

time

Updated: April 10, 2022

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

Category: Action Commands, CPPTRAJ

xtalsymm

Updated: April 10, 2022

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

Category: Action Commands, CPPTRAJ

fiximagedbonds

Posted: April 10, 2022

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

Category: Action Commands, CPPTRAJ