Provided by: gromacs-data_2019.3-2_all bug

NAME

       gmx-make_edi - Generate input files for essential dynamics sampling

SYNOPSIS

          gmx make_edi [-f [<.trr/.cpt/...>]] [-eig [<.xvg>]]
                       [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                       [-tar [<.gro/.g96/...>]] [-ori [<.gro/.g96/...>]]
                       [-o [<.edi>]] [-xvg <enum>] [-mon <string>]
                       [-linfix <string>] [-linacc <string>] [-radfix <string>]
                       [-radacc <string>] [-radcon <string>] [-flood <string>]
                       [-outfrq <int>] [-slope <real>] [-linstep <string>]
                       [-accdir <string>] [-radstep <real>] [-maxedsteps <int>]
                       [-eqsteps <int>] [-deltaF0 <real>] [-deltaF <real>]
                       [-tau <real>] [-Eflnull <real>] [-T <real>]
                       [-alpha <real>] [-[no]restrain] [-[no]hessian]
                       [-[no]harmonic] [-constF <string>]

DESCRIPTION

       gmx  make_edi  generates  an  essential  dynamics (ED) sampling input file to be used with
       mdrun based on eigenvectors of a covariance matrix (gmx covar)  or  from  a  normal  modes
       analysis (gmx nmeig).  ED sampling can be used to manipulate the position along collective
       coordinates  (eigenvectors)  of   (biological)   macromolecules   during   a   simulation.
       Particularly,  it  may  be  used  to  enhance the sampling efficiency of MD simulations by
       stimulating the system to explore new regions along these collective coordinates. A number
       of  different  algorithms  are  implemented  to  drive  the  system along the eigenvectors
       (-linfix, -linacc, -radfix, -radacc, -radcon), to keep the position along a  certain  (set
       of)  coordinate(s)  fixed  (-linfix),  or to only monitor the projections of the positions
       onto these coordinates (-mon).

       References:

       A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F.  van  Aalten  and  H.J.C.  Berendsen;  An
       efficient method for sampling the essential subspace of proteins., J. Biomol. Struct. Dyn.
       13:615-626 (1996)

       B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen;  Towards  an  exhaustive
       sampling  of  the configurational spaces of the two forms of the peptide hormone guanylin,
       J. Biomol. Struct. Dyn. 13 : 741-751 (1996)

       B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C. Berendsen; An  extended
       sampling  of  the  configurational space of HPr from E. coli Proteins: Struct. Funct. Gen.
       26: 314-322 (1996)

       You will be prompted for one or more index groups that  correspond  to  the  eigenvectors,
       reference structure, target positions, etc.

       -mon: monitor projections of the coordinates onto selected eigenvectors.

       -linfix: perform fixed-step linear expansion along selected eigenvectors.

       -linacc:  perform  acceptance linear expansion along selected eigenvectors.  (steps in the
       desired directions will be accepted, others will be rejected).

       -radfix: perform fixed-step radius expansion along selected eigenvectors.

       -radacc: perform acceptance radius expansion along selected eigenvectors.  (steps  in  the
       desired  direction  will  be  accepted,  others  will  be rejected).  Note: by default the
       starting MD structure will be taken as origin of the  first  expansion  cycle  for  radius
       expansion. If -ori is specified, you will be able to read in a structure file that defines
       an external origin.

       -radcon: perform acceptance radius  contraction  along  selected  eigenvectors  towards  a
       target structure specified with -tar.

       NOTE: each eigenvector can be selected only once.

       -outfrq: frequency (in steps) of writing out projections etc. to .xvg file

       -slope:  minimal  slope  in  acceptance  radius  expansion.  A new expansion cycle will be
       started if the spontaneous increase of the radius (in nm/step)  is  less  than  the  value
       specified.

       -maxedsteps:  maximum  number of steps per cycle in radius expansion before a new cycle is
       started.

       Note on the parallel implementation: since ED sampling is  a  ‘global’  thing  (collective
       coordinates   etc.),   at   least   on  the  ‘protein’  side,  ED  sampling  is  not  very
       parallel-friendly from an implementation point of view. Because parallel ED requires  some
       extra  communication,  expect  the  performance  to  be  lower as in a free MD simulation,
       especially on a large number of ranks and/or when the ED group contains a lot of atoms.

       Please also note that if your ED group contains more than a single protein, then the  .tpr
       file  must  contain  the  correct  PBC representation of the ED group.  Take a look on the
       initial RMSD from the reference structure, which is  printed  out  at  the  start  of  the
       simulation; if this is much higher than expected, one of the ED molecules might be shifted
       by a box vector.

       All ED-related output of mdrun (specify with -eo) is written to a .xvg file as a  function
       of time in intervals of OUTFRQ steps.

       Note  that  you  can  impose  multiple  ED constraints and flooding potentials in a single
       simulation (on different molecules) if several .edi files  were  concatenated  first.  The
       constraints  are applied in the order they appear in the .edi file.  Depending on what was
       specified in the .edi input file, the output file contains for each ED dataset

          · the RMSD of the fitted molecule to the reference structure  (for  atoms  involved  in
            fitting prior to calculating the ED constraints)

          · projections of the positions onto selected eigenvectors

       FLOODING:

       with  -flood, you can specify which eigenvectors are used to compute a flooding potential,
       which will lead to extra forces expelling the structure out of the region described by the
       covariance  matrix. If you switch -restrain the potential is inverted and the structure is
       kept in that region.

       The origin is normally the average structure stored in the eigvec.trr  file.   It  can  be
       changed  with  -ori to an arbitrary position in configuration space.  With -tau, -deltaF0,
       and -Eflnull you control the flooding behaviour.  Efl is  the  flooding  strength,  it  is
       updated  according to the rule of adaptive flooding.  Tau is the time constant of adaptive
       flooding, high tau means slow adaption (i.e. growth).  DeltaF0 is  the  flooding  strength
       you want to reach after tau ps of simulation.  To use constant Efl set -tau to zero.

       -alpha  is  a fudge parameter to control the width of the flooding potential. A value of 2
       has been found to give good results for most  standard  cases  in  flooding  of  proteins.
       alpha  basically accounts for incomplete sampling, if you sampled further the width of the
       ensemble would increase, this is mimicked by alpha > 1.  For restraining, alpha  <  1  can
       give you smaller width in the restraining potential.

       RESTART and FLOODING: If you want to restart a crashed flooding simulation please find the
       values deltaF and Efl in the output file and manually put them into the  .edi  file  under
       DELTA_F0 and EFL_NULL.

OPTIONS

       Options to specify input files:

       -f [<.trr/.cpt/…>] (eigenvec.trr)
              Full precision trajectory: trr cpt tng

       -eig [<.xvg>] (eigenval.xvg) (Optional)
              xvgr/xmgr file

       -s [<.tpr/.gro/…>] (topol.tpr)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       -tar [<.gro/.g96/…>] (target.gro) (Optional)
              Structure file: gro g96 pdb brk ent esp tpr

       -ori [<.gro/.g96/…>] (origin.gro) (Optional)
              Structure file: gro g96 pdb brk ent esp tpr

       Options to specify output files:

       -o [<.edi>] (sam.edi)
              ED sampling input

       Other options:

       -xvg <enum> (xmgrace)
              xvg plot formatting: xmgrace, xmgr, none

       -mon <string>
              Indices  of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11
              21 31 … 91

       -linfix <string>
              Indices of eigenvectors for fixed increment linear sampling

       -linacc <string>
              Indices of eigenvectors for acceptance linear sampling

       -radfix <string>
              Indices of eigenvectors for fixed increment radius expansion

       -radacc <string>
              Indices of eigenvectors for acceptance radius expansion

       -radcon <string>
              Indices of eigenvectors for acceptance radius contraction

       -flood <string>
              Indices of eigenvectors for flooding

       -outfrq <int> (100)
              Frequency (in steps) of writing output in .xvg file

       -slope <real> (0)
              Minimal slope in acceptance radius expansion

       -linstep <string>
              Stepsizes (nm/step) for fixed increment linear sampling (put in  quotes!  “1.0  2.3
              5.1 -3.1”)

       -accdir <string>
              Directions  for  acceptance linear sampling - only sign counts! (put in quotes! “-1
              +1 -1.1”)

       -radstep <real> (0)
              Stepsize (nm/step) for fixed increment radius expansion

       -maxedsteps <int> (0)
              Maximum number of steps per cycle

       -eqsteps <int> (0)
              Number of steps to run without any perturbations

       -deltaF0 <real> (150)
              Target destabilization energy for flooding

       -deltaF <real> (0)
              Start deltaF with this parameter -  default  0,  nonzero  values  only  needed  for
              restart

       -tau <real> (0.1)
              Coupling  constant  for  adaption  of  flooding  strength according to deltaF0, 0 =
              infinity i.e. constant flooding strength

       -Eflnull <real> (0)
              The starting value of the flooding  strength.  The  flooding  strength  is  updated
              according  to  the  adaptive  flooding scheme. For a constant flooding strength use
              -tau 0.

       -T <real> (300)
              T is temperature, the value is needed if you want to do flooding

       -alpha <real> (1)
              Scale width of gaussian flooding potential with alpha^2

       -[no]restrain (no)
              Use  the  flooding  potential  with  inverted  sign  ->  effects  as  quasiharmonic
              restraining potential

       -[no]hessian (no)
              The eigenvectors and eigenvalues are from a Hessian matrix

       -[no]harmonic (no)
              The eigenvalues are interpreted as spring constant

       -constF <string>
              Constant force flooding: manually set the forces for the eigenvectors selected with
              -flood (put in quotes! “1.0 2.3 5.1 -3.1”). No other flooding parameters are needed
              when specifying the forces directly.

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2019, GROMACS development team