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**PROGRAM:**

**NAME**

gmx-anaeig - Analyze eigenvectors/normal modes

**SYNOPSIS**

gmx anaeig [

**-v**

__[<.trr/.cpt/...>]__] [

**-v2**

__[<.trr/.cpt/...>]__]

[

**-f**

__[<.xtc/.trr/...>]__] [

**-s**

__[<.tpr/.gro/...>]__]

[

**-n**

__[<.ndx>]__] [

**-eig**

__[<.xvg>]__] [

**-eig2**

__[<.xvg>]__]

[

**-comp**

__[<.xvg>]__] [

**-rmsf**

__[<.xvg>]__] [

**-proj**

__[<.xvg>]__]

[

**-2d**

__[<.xvg>]__] [

**-3d**

__[<.gro/.g96/...>]__]

[

**-filt**

__[<.xtc/.trr/...>]__] [

**-extr**

__[<.xtc/.trr/...>]__]

[

**-over**

__[<.xvg>]__] [

**-inpr**

__[<.xpm>]__] [

**-b**

__<time>__] [

**-e**

__<time>__]

[

**-dt**

__<time>__] [

**-tu**

__<enum>__] [

**-[no]w**] [

**-xvg**

__<enum>__]

[

**-first**

__<int>__] [

**-last**

__<int>__] [

**-skip**

__<int>__] [

**-max**

__<real>__]

[

**-nframes**

__<int>__] [

**-[no]split**] [

**-[no]entropy**]

[

**-temp**

__<real>__] [

**-nevskip**

__<int>__]

**DESCRIPTION**

**gmx**

**anaeig**analyzes eigenvectors. The eigenvectors can be of a covariance matrix (

**gmx**

**covar**) or of a Normal Modes analysis (

**gmx**

**nmeig**).

When a trajectory is projected on eigenvectors, all structures are fitted to the structure

in the eigenvector file, if present, otherwise to the structure in the structure file.

When no run input file is supplied, periodicity will not be taken into account. Most

analyses are performed on eigenvectors

**-first**to

**-last**, but when

**-first**is set to -1 you

will be prompted for a selection.

**-comp**: plot the vector components per atom of eigenvectors

**-first**to

**-last**.

**-rmsf**: plot the RMS fluctuation per atom of eigenvectors

**-first**to

**-last**(requires

**-eig**).

**-proj**: calculate projections of a trajectory on eigenvectors

**-first**to

**-last**. The

projections of a trajectory on the eigenvectors of its covariance matrix are called

principal components (pc's). It is often useful to check the cosine content of the pc's,

since the pc's of random diffusion are cosines with the number of periods equal to half

the pc index. The cosine content of the pc's can be calculated with the program

**gmx**

**analyze**.

**-2d**: calculate a 2d projection of a trajectory on eigenvectors

**-first**and

**-last**.

**-3d**: calculate a 3d projection of a trajectory on the first three selected eigenvectors.

**-filt**: filter the trajectory to show only the motion along eigenvectors

**-first**to

**-last**.

**-extr**: calculate the two extreme projections along a trajectory on the average structure

and interpolate

**-nframes**frames between them, or set your own extremes with

**-max**. The

eigenvector

**-first**will be written unless

**-first**and

**-last**have been set explicitly, in

which case all eigenvectors will be written to separate files. Chain identifiers will be

added when writing a

__.pdb__file with two or three structures (you can use

**rasmol**

**-nmrpdb**to

view such a

__.pdb__file).

**Overlap**

**calculations**

**between**

**covariance**

**analysis**

**Note:**the analysis should use the same fitting structure

**-over**: calculate the subspace overlap of the eigenvectors in file

**-v2**with eigenvectors

**-first**to

**-last**in file

**-v**.

**-inpr**: calculate a matrix of inner-products between eigenvectors in files

**-v**and

**-v2**. All

eigenvectors of both files will be used unless

**-first**and

**-last**have been set explicitly.

When

**-v**,

**-eig**,

**-v2**and

**-eig2**are given, a single number for the overlap between the

covariance matrices is generated. The formulas are:

difference = sqrt(tr((sqrt(M1) - sqrt(M2))^2))

normalized overlap = 1 - difference/sqrt(tr(M1) + tr(M2))

shape overlap = 1 - sqrt(tr((sqrt(M1/tr(M1)) - sqrt(M2/tr(M2)))^2))

where M1 and M2 are the two covariance matrices and tr is the trace of a matrix. The

numbers are proportional to the overlap of the square root of the fluctuations. The

normalized overlap is the most useful number, it is 1 for identical matrices and 0 when

the sampled subspaces are orthogonal.

When the

**-entropy**flag is given an entropy estimate will be computed based on the

Quasiharmonic approach and based on Schlitter's formula.

**OPTIONS**

Options to specify input files:

**-v**

**[<.trr/.cpt/...>]**

**(eigenvec.trr)**

Full precision trajectory:

__trr__

__cpt__

__tng__

**-v2**

**[<.trr/.cpt/...>]**

**(eigenvec2.trr)**

**(Optional)**

Full precision trajectory:

__trr__

__cpt__

__tng__

**-f**

**[<.xtc/.trr/...>]**

**(traj.xtc)**

**(Optional)**

Trajectory:

__xtc__

__trr__

__cpt__

__gro__

__g96__

__pdb__

__tng__

**-s**

**[<.tpr/.gro/...>]**

**(topol.tpr)**

**(Optional)**

Structure+mass(db):

__tpr__

__gro__

__g96__

__pdb__brk ent

**-n**

**[<.ndx>]**

**(index.ndx)**

**(Optional)**

Index file

**-eig**

**[<.xvg>]**

**(eigenval.xvg)**

**(Optional)**

xvgr/xmgr file

**-eig2**

**[<.xvg>]**

**(eigenval2.xvg)**

**(Optional)**

xvgr/xmgr file

Options to specify output files:

**-comp**

**[<.xvg>]**

**(eigcomp.xvg)**

**(Optional)**

xvgr/xmgr file

**-rmsf**

**[<.xvg>]**

**(eigrmsf.xvg)**

**(Optional)**

xvgr/xmgr file

**-proj**

**[<.xvg>]**

**(proj.xvg)**

**(Optional)**

xvgr/xmgr file

**-2d**

**[<.xvg>]**

**(2dproj.xvg)**

**(Optional)**

xvgr/xmgr file

**-3d**

**[<.gro/.g96/...>]**

**(3dproj.pdb)**

**(Optional)**

Structure file:

__gro__

__g96__

__pdb__brk ent esp

**-filt**

**[<.xtc/.trr/...>]**

**(filtered.xtc)**

**(Optional)**

Trajectory:

__xtc__

__trr__

__cpt__

__gro__

__g96__

__pdb__

__tng__

**-extr**

**[<.xtc/.trr/...>]**

**(extreme.pdb)**

**(Optional)**

Trajectory:

__xtc__

__trr__

__cpt__

__gro__

__g96__

__pdb__

__tng__

**-over**

**[<.xvg>]**

**(overlap.xvg)**

**(Optional)**

xvgr/xmgr file

**-inpr**

**[<.xpm>]**

**(inprod.xpm)**

**(Optional)**

X PixMap compatible matrix file

Other options:

**-b**

**<time>**

**(0)**

First frame (ps) to read from trajectory

**-e**

**<time>**

**(0)**

Last frame (ps) to read from trajectory

**-dt**

**<time>**

**(0)**

Only use frame when t MOD dt = first time (ps)

**-tu**

**<enum>**

**(ps)**

Unit for time values: fs, ps, ns, us, ms, s

**-[no]w**

**(no)**

View output

__.xvg__,

__.xpm__,

__.eps__and

__.pdb__files

**-xvg**

**<enum>**

xvg plot formatting: xmgrace, xmgr, none

**-first**

**<int>**

**(1)**

First eigenvector for analysis (-1 is select)

**-last**

**<int>**

**(-1)**

Last eigenvector for analysis (-1 is till the last)

**-skip**

**<int>**

**(1)**

Only analyse every nr-th frame

**-max**

**<real>**

**(0)**

Maximum for projection of the eigenvector on the average structure, max=0 gives the

extremes

**-nframes**

**<int>**

**(2)**

Number of frames for the extremes output

**-[no]split**

**(no)**

Split eigenvector projections where time is zero

**-[no]entropy**

**(no)**

Compute entropy according to the Quasiharmonic formula or Schlitter's method.

**-temp**

**<real>**

**(298.15)**

Temperature for entropy calculations

**-nevskip**

**<int>**

**(6)**

Number of eigenvalues to skip when computing the entropy due to the quasi harmonic

approximation. When you do a rotational and/or translational fit prior to the

covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and

which should not be taken into account when computing the entropy.

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