CPPTRAJ Manual

User Manual:

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Introduction
- Manual Syntax Format
Running Cpptraj
General Concepts
Variables and Control Structures
- for
- set
- show
Data Sets and Data Files
- Data Set Selection Syntax
- Data Set Math
Data File Options
Coordinates (COORDS) Data Set Commands
General Commands
Topology File Commands
Trajectory File Commands
Action Commands
Analysis Commands
Analysis Examples
- Cartesian covariance matrix calculation and projection (PCA)
- Dihedral covariance matrix calculation and projection for backbone phi/psi (PCA)

AvgCorr(a, b) = PVa(i)·Vb(i)

N

8

3π2

8

3π2

hF lucti=PAtomF lucti∗M assi

PMassi

2nD = lim

t→∞

MSD

t

3

3

i Xi,norm

Xi,dens Xi,norm =ρiXi,dens ρi

Xtot =Vvoxel PiXi,dens Vvoxel

ni

×

3

3

3

3

3

3

3

3

3

qtet

i

qtet(i) = 1 −3

8P3

j=1 P4

k=j+1(cosφijk +1

3)2j k

i φijk

i j k

i j j > i

i j

3

−3

Q Qref erence =PniQi

Pni

Qini

i ρi

ρogi=ρi/ρo

R

ER

W W

ER

W W = 2(Pi∈REi,W W −Pi∈RPj∈R,j>i Ei,j,W W )

i∈R i R Ei,W W

i Ei,j,W W

i j

Eelec =kqiqj

rij 1−r2

ij

r2

cut !2

SxSySz

SzCn−1Cn+1 Sx

Cn−1−CnCn−Cn+1 Sy

Sc = 0.5<

3 cos(2θ)>−1θ

SxSySz|SCD|= 0.5×Sz|SCD|=

−(2Sx+Sy)/3

−

Density ∗4π

3(R+dR)3−R3

−

− −

0.6022

MrMr

8

3π2

8

3π2

−1

Gi=−kBTln Ni

NMax 

τm

Cl(t= 0) = Pl(t= 0) = 1.0

τm

τm

|

C(i) = Pj<N −i

j=0 exp(−RMSD(j,j+i))

N−i

1/r6

1/r6

Cl≡< Pl/(r(0)3r(τ)3)>

<1/(r(0)3r(τ)3)> Pl

Cl(t= 0) = Pl(t= 0) = 1.0

χ2

2

S0S02(nb−1)ds

S=S02jds;j=

0,1,2, . . . , nb −1

µkXn

fk=1

N

N−1

X

n=0

exp −2πikn

NXn

|Wi,k|2σ2

σ2µkχ2

2/2

|Wi,k|2