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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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