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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 (pcas). It is often useful to check the cosine content of the pcas, since the pcas of ran- dom diffusion are cosines with the number of periods equal to half the pc index. The cosine content of the pcas 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 Schlitteras formula. OPTIONS Options to specify input files: -v [<.trr/.cpt/^a|>] (eigenvec.trr) Full precision trajectory: trr cpt tng -v2 [<.trr/.cpt/^a|>] (eigenvec2.trr) (Optional) Full precision trajectory: trr cpt tng -f [<.xtc/.trr/^a|>] (traj.xtc) (Optional) Trajectory: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/^a|>] (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/^a|>] (3dproj.pdb) (Optional) Structure file: gro g96 pdb brk ent esp -filt [<.xtc/.trr/^a|>] (filtered.xtc) (Optional) Trajectory: xtc trr cpt gro g96 pdb tng -extr [<.xtc/.trr/^a|>] (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 Schlitteras 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 2020, GROMACS development team 2020.4 Oct 06, 2020 GMX-ANAEIG(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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