CPPTRAJ Manual
User Manual:
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Page Count: 207 [warning: Documents this large are best viewed by clicking the View PDF Link!]
- Introduction
- Running Cpptraj
- General Concepts
- Variables and Control Structures
- Data Sets and Data Files
- Data File Options
- Coordinates (COORDS) Data Set Commands
- General Commands
- Topology File Commands
- Trajectory File Commands
- Action Commands
- angle
- areapermol
- atomiccorr
- atomicfluct | rmsf
- atommap
- autoimage
- average
- avgcoord
- bounds
- box
- center
- check | checkoverlap | checkstructure
- checkchirality
- closest | closestwaters
- cluster
- clusterdihedral
- contacts
- createcrd
- createreservoir
- density
- diffusion
- dihedral
- dihedralscan
- dipole
- distance
- drms | drmsd (distance RMSD)
- dssp
- energy
- esander
- filter
- fixatomorder
- fiximagedbonds
- gist (Grid Inhomogeneous Solvation Theory)
- grid
- hbond
- image
- jcoupling
- lessplit
- lie
- lipidorder
- lipidscd
- makestructure
- mask
- matrix
- mindist
- minimage
- molsurf
- multidihedral
- multivector
- nastruct
- nativecontacts
- outtraj
- pairdist
- pairwise
- principal
- projection
- pucker
- radgyr | rog
- radial | rdf
- randomizeions
- replicatecell
- rms | rmsd
- rms2d | 2drms
- rmsavgcorr
- rmsf | atomicfluct
- rotate
- rotdif
- runavg | runningaverage
- scale
- secstruct
- spam
- setvelocity
- stfcdiffusion
- strip
- surf
- symmrmsd
- temperature
- trans | translate
- unstrip
- unwrap
- vector
- velocityautocorr
- volmap
- volume
- watershell
- Analysis Commands
- autocorr
- avg
- calcstate
- cluster
- cphstats
- corr | correlationcoe
- crank | crankshaft
- crdfluct
- crosscorr
- curvefit
- diagmatrix
- divergence
- fft
- hist | histogram
- integrate
- ired
- kde
- lifetime
- lowestcurve
- meltcurve
- modes
- multicurve
- multihist
- phipsi
- regress
- remlog
- rms2d | 2drms
- rmsavgcorr
- rotdif
- runningavg
- spline
- statistics | stat
- ti
- timecorr
- vectormath
- wavelet
- Analysis Examples