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GMX-ANAEIG(1) GROMACS GMX-ANAEIG(1)NAMEgmx-anaeig - Analyze eigenvectors/normal modesSYNOPSISgmx 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_]DESCRIPTIONgmxanaeiganalyzes 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-firstto-last, but when-firstis set to -1 you will be prompted for a selection.-comp: plot the vector components per atom of eigenvectors-firstto-last.-rmsf: plot the RMS fluctuation per atom of eigenvectors-firstto-last(requires-eig).-proj: calculate projections of a trajectory on eigenvectors-firstto-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-firstand-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-firstto-last.-extr: calculate the two extreme projections along a trajectory on the average structure and interpolate-nframesframes between them, or set your own extremes with-max. The eigenvector-firstwill be written un- less-firstand-lasthave 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 userasmol-nmrpdbto view such a .pdb file).OverlapcalculationsbetweencovarianceanalysisNote:the analysis should use the same fitting structure-over: calculate the subspace overlap of the eigenvectors in file-v2with eigenvectors-firstto-lastin file-v.-inpr: calculate a matrix of inner-products between eigenvectors in files-vand-v2. All eigenvectors of both files will be used unless-firstand-lasthave been set explicitly. When-vand-v2are 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-eig2are 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-entropyflag is given an entropy estimate will be computed based on the Quasiharmonic approach and based on Schlitteras formula.OPTIONSOptions 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 ALSOgmx(1)More information about GROMACS is available at <-http://www.gromacs.org/>.COPYRIGHT2020, GROMACS development team 2020.3 Jul 09, 2020 GMX-ANAEIG(1)

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