man g_anaeig (Commandes) - g_anaeig VERSION 3.3_beta_20050823
NAME
g_anaeig VERSION 3.3_beta_20050823
SYNOPSIS
g_anaeig -v eigenvec.trr -v2 eigenvec2.trr -f traj.xtc -s topol.tpr -n index.ndx -eig eigenval.xvg -eig2 eigenval2.xvg -comp eigcomp.xvg -rmsf eigrmsf.xvg -proj proj.xvg -2d 2dproj.xvg -3d 3dproj.pdb -filt filtered.xtc -extr extreme.pdb -over overlap.xvg -inpr inprod.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -first int -last int -skip int -max real -nframes int -[no]split
DESCRIPTION
g_anaeig analyzes eigenvectors. The eigenvectors can be of a covariance matrix ( g_covar ) or of a Normal Modes anaysis ( g_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 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
g_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 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 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.
FILES
-v eigenvec.trr Input Full precision trajectory: trr trj
-v2 eigenvec2.trr Input, Opt. Full precision trajectory: trr trj
-f traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-n index.ndx Input, Opt. Index file
-eig eigenval.xvg Input, Opt. xvgr/xmgr file
-eig2 eigenval2.xvg Input, Opt. xvgr/xmgr file
-comp eigcomp.xvg Output, Opt. xvgr/xmgr file
-rmsf eigrmsf.xvg Output, Opt. xvgr/xmgr file
-proj proj.xvg Output, Opt. xvgr/xmgr file
-2d 2dproj.xvg Output, Opt. xvgr/xmgr file
-3d 3dproj.pdb Output, Opt. Generic structure: gro g96 pdb xml
-filt filtered.xtc Output, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-extr extreme.pdb Output, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-over overlap.xvg Output, Opt. xvgr/xmgr file
-inpr inprod.xpm Output, Opt. X PixMap compatible matrix file
OTHER OPTIONS
-[no]h no Print help info and quit
-nice int 19 Set the nicelevel
-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 Time unit: ps , fs , ns , us , ms , s , m or h
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-first int 1 First eigenvector for analysis (-1 is select)
-last int 8 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