Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages


home | help

       gmx-anaeig - Analyze eigenvectors/normal	modes

	  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_]

       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

       -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 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.


       More    information    about    GROMACS	  is	available    at	    <->.

       2020, GROMACS development team

2020.4				 Oct 06, 2020			 GMX-ANAEIG(1)


Want to link to this manual page? Use this URL:

home | help