gmx-make_edi(1) GROMACS Manual gmx-make_edi(1)NAMEgmx-make_edi - Generate input files for essential dynamics sampling
SYNOPSIS
gmx make_edi [-f [<.trr/.cpt/...>]] [-eig [<.xvg>]]
[-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-tar [<.gro/.g96/...>]] [-ori [<.gro/.g96/...>]]
[-o [<.edi>]] [-nice <int>] [-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 (eigenvec‐
tors) 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 eigenvec‐
tors.
-linfix: perform fixed-step linear expansion along selected eigenvec‐
tors.
-linacc: perform acceptance linear expansion along selected eigenvec‐
tors. (steps in the desired directions will be accepted, others will be
rejected).
-radfix: perform fixed-step radius expansion along selected eigenvec‐
tors.
-radacc: perform acceptance radius expansion along selected eigenvec‐
tors. (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 eigenvec‐
tors 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 pro‐
tein, then the .tpr file must contain the correct PBC representation of
the ED group. Take a look on the initial RMSD from the reference struc‐
ture, 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 poten‐
tials 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) * projec‐
tions 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 configu‐
ration space. With -tau, -deltaF0, and -Eflnull you control the flood‐
ing 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 poten‐
tial. A value of 2 has been found to give good results for most stan‐
dard cases in flooding of proteins. alpha basically accounts for incom‐
plete 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 simula‐
tion please find the values deltaF and Efl in the output file and manu‐
ally put them into the .edi file under DELTA_F0 and EFL_NULL.
OPTIONS
Options to specify input and output files:
-f [<.trr/.cpt/...>] (eigenvec.trr) (Input)
Full precision trajectory: trr cpt trj tng
-eig [<.xvg>] (eigenval.xvg) (Input, Optional)
xvgr/xmgr file
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-tar [<.gro/.g96/...>] (target.gro) (Input, Optional)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-ori [<.gro/.g96/...>] (origin.gro) (Input, Optional)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-o [<.edi>] (sam.edi) (Output)
ED sampling input
Other options:
-nice <int> (0)
Set the nicelevel
-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)
Freqency (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 alpha2
-[no]restrain (no)
Use the flooding potential with inverted sign - effects as quasi‐
harmonic 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 eigenvec‐
tors 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-make_edi(1)
