GMX-ANAEIG(1) | GROMACS | GMX-ANAEIG(1) |

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>]

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))

**-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

**-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

**-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> (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 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.

September 15, 2017 | 2016.4 |