FreeBSD Manual Pages
GMX-ANAEIG(1) GROMACS GMX-ANAEIG(1) 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 covari- ance matrix (gmx covar) or of a Normal Modes analysis (gmx nmeig). When a trajectory is projected on eigenvectors, all structures are fit- ted to the structure in the eigenvector file, if present, otherwise to the structure in the structure file. When no run input file is sup- plied, 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 co- variance 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 ran- dom 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 se- lected 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 un- less -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 and -v2 are given, a single number for the overlap between the covariance matrices is generated. Note that the eigenvalues are by de- fault read from the timestamp field in the eigenvector input files, but when -eig, or -eig2 are given, the corresponding eigenvalues are used instead. 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) Time of first frame to read from trajectory (default unit ps) -e <time> (0) Time of last frame to read from trajectory (default unit ps) -dt <time> (0) Only use frame when t MOD dt = first time (default unit 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> (xmgrace) 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 struc- ture, 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. SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-ANAEIG(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
Want to link to this manual page? Use this URL:
<https://man.freebsd.org/cgi/man.cgi?query=gmx-anaeig&sektion=1&manpath=FreeBSD+Ports+14.3.quarterly>