Commands to perform analysis on frames and topology.
Actions in CPPTRAJ operate on frames read in by the trajin or ensemble commands one at a time and extract derived data, modify the coordinates/topology in some way, or both. Most Actions in CPPTRAJ function exactly the way they do in ptraj and are backwardscompatible. Some Action commands in CPPTRAJ have extra functionality compared to ptraj (such as the perresidue RMSD function of the rmsd Action, or the ability to write out stripped topologies for visualization in the strip Action), while other Actions produce slightly different output (like the hbond/secstruct Actions).
Unlike some other command types, when an Action command is issued it is by default added to the Action queue and is not executed until trajectory processing is started (e.g. by a run
or go
command). However, Actions can be executed immediately on COORDS data sets via the crdaction command.
When a frame is modified by an Action, it is modified for every Action that follows them during trajectory processing. For example, given a solvated system with water residues named WAT and the following Action commands:
rmsd R1 first :WAT out waterrmsd.dat strip :WAT rmsd R2 first :WAT out waterrmsd2.dat
the first rms
command will be valid, but the second rms
command will not since all residues named WAT are removed from the state by the strip command. Note that for commands which can use a reference mask as well as a target mask (e.g. rms, drmsd, symmrmsd, etc.) there must be a 1 to 1 correspondence between the atoms in each mask, i.e. the number of atoms and the ordering of selected atoms must be the same.
The following Actions are available. If an Action may modify coordinate/topology information for subsequent Actions it is denoted with an X in the Mod column.
Command  Description  Mod 
addatom  Add a dummy atom.  
align  Align structure to a reference.  
angle  Calculate the angle between three points.  
areapermol  Calculate area per molecule for molecules in a specified plane.  
atomiccorr  Calculate average correlation between motions of specified atoms.  
atomicfluct, rmsf  Calculate root mean square fluctuation of specified atoms/residues.  
atommap  Attempt to create a map between atoms in molecules with different atom ordering.  X 
autoimage  Automatically reimage coordinates.  X 
average  Calculate average structure.  
avgbox  Calculate average unit cell (box), primarily for unwrapping NPT trajectories.  
avgcoord  This command is deprecated. Use vector center (optionally with keyword magnitude ) instead. 

bounds  Calculate the min/max coordinates for specified atoms. Can be used to create grid data sets.  
box  Set or overwrite box information for frames.  
center  Center specified coordinates to box center or onto reference structure.  X 
check, checkoverlap, checkstructure  Check for bad atomic overlaps or bond lengths. Can be used to skip corrupted frames.  
checkchirality  Report chirality around alpha carbons in amino acids (L, D).  
closest, closestwaters  Retain only the specified number of solvent molecules closest to specified solute.  X 
clusterdihedral  Assign frames into clusters based on binning of backbone dihedral angles in amino acids.  
contacts  Older version of nativecontacts, retained for backwards compatibility.  
createcrd  Create a COORDS data set from input frames.  
createreservoir  Create a structure reservoir for use with reservoir REMD simulations.  
density  Calculate density along a coordinate.  
diffusion  Calculate translational diffusion of molecules.  
dihedral  Calculate the dihedral angle using four points.  
dihrms, dihedralrms  Calculate the RMSD of dihedrals to dihedrals in a reference structure.  
dipole  Bin dipoles of solvent molecules in 3D grid. Not well tested, may be obsolete.  
distance  Calculate the distance between two points.  
drms, drmsd  Calculate the RMSD of distance pairs within selected atoms.  
dssp, secstruct  Calculate secondary structure content using the DSSP algorithm  
energy  Calculate simple bond, angle, dihedral, and nonbonded energy terms (no PME).  
esander  Calculate energies using via SANDER; requires compilation with the SANDER API.  
filter  Filter frames for subsequent Actions using data sets and user defined criteria.  
fixatomorder  Fix atom ordering so that all atoms in molecules are sequential.  X 
fiximagedbonds  Fix bonds which have been split across periodic boundaries by imaging.  
gist  Perform grid inhomogenous solvation theory.  
grid  Bin selected atoms on a 3D grid.  
hbond  Calculate hydrogen bonds using geometric criteria.  
image  Reimage coordinates. The autoimage command typically provides better results.  X 
jcoupling  Calculate Jcoupling values from specified dihedral angles.  
keep  Keep specied atoms in system.  X 
lessplit  Split/average frames from LES trajectories.  
lie  Calculate linear interaction energy between userspecified ligand and surroundings.  
lipidorder  Calculate order parameters for lipids in planar membranes.  
lipidscd  Calculate lipid order parameters SCD(<P2>) for lipid chains. Automatically identifies lipids.  
makestructure  Modify structure by applying dihedral values to specified residues.  X 
mask  Print the results of selection by specified atom mask. Good for distancebased masks.  
matrix  Calculate a matrix of the specified type from input coordinates.  
minimage  Calculate minimum nonself imaged distance between atoms in specified masks.  
molsurf  Calculate Connolly surface area of specified atoms. Cannot do partial surface areas.  
multidihedral  Calculate multiple dihedral angles of specified/given types.  
multipucker  Calculate specified pucker types for residues in given range..  
multivector  Calculate multiple vectors between specified atoms.  
nastruct  Perform nucelic acid structure analysis.  
nativecontacts  Calculate native contacts within a region or between two regions using a given reference. Can also be used to get min/max distances between groups of atoms.  
outtraj  Write frames to a trajectory file within a list of Actions.  
pairdist  Calculate pair distribution function.  
pairwise  Calculate pairwise nonbonded energies.  
principal  Calculate and optionally align system along principal axes.  X 
projection  Project coordinates along given eigenvectors.  
pucker  Calculate ring pucker using five or six points.  
radgyr, rog  Calculate radius of gyration (and optionally tensor) for specified atoms.  
radial, rdf  Calculate radial distribution function.  
randomizeions  Swap specified ions with randomly selected solvent molecules.  X 
remap  Remap atoms according to a given data set.  
replicatecell  Replicate unit cell in specified (or all) directions for specfied atoms and write to trajectory.  
rms, rmsd  Perform best fit of coordinates to reference and calculate coordinate RMSD. X Fitting can be disabled.  X 
rotate  Rotate the system around X/Y/Z axes, a specified axis, or via given rotation matrices.  X 
runavg, runningaverage  Calculate the running average of coordinates over specified window size.  X 
scale  Scale coordinates in X/Y/Z directions by specified factors.  X 
setvelocity  Set velocities for specified atoms using Maxwellian distribution based on given temperature.  
spam  SPAM method for estimating relative free energies of waters in hydration shell around proteins.  X 
stfcdiffusion  Alternative translational diffusion calculation which can calculate diffusion in specified regions.  
strip  Remove specified atoms from the system.  
surf  Calculate the LCPO surface area of specified atoms. Can do partial surface areas.  
symmrmsd  Calculate symmetrycorrected RMSD.  X 
temperature  Calculate system temperature using velocities of specified atoms.  
time  Add/remove/modify time information in frames.  
trans, translate  Translate specified atoms by specified amounts in X/Y/Z directions.  X 
unstrip  Undo all previous strip Action commands.  
unwrap  Reverse of image; unwrap selected atoms so they have continuous trajectories.  X 
vector  Calculate various types of vector quantities.  
velocityautocorr  Calculate velocity autocorrelation function.  
volmap  Create volumetric map for specified coordinates; similar to grid but takes into account atomic radii. Similar to VMD volmap.  
volume  Calculate unit cell volume.  
watershell  Calculate the number of waters in the first and second solvation shells based on distance criteria.  
xtalsymm  Reimage coordinates based on crystal space group symmetry operations and asymmetric unit volume.  X 