make_edi - generate input files for essential dynamics sampling
make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -n index.ndx
-tar target.gro -ori origin.gro -o sam.edi -[no]h -nice int -[no]xvgr
-mon string -linfix string -linacc string -flood string -radfix string
-radacc string -radcon string -outfrq int -slope real -maxedsteps int
-deltaF0 real -deltaF real -tau real -eqsteps int -Eflnull real -T real
-alpha real -linstep string -accdir string -radstep real -[no]restrain
make_edi generates an essential dynamics (ED) sampling input file to
be used with mdrun based on eigenvectors of a covariance matrix (
g_covar) or from a normal modes anaysis ( g_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).
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 :
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
-linfix: perform fixed-step linear expansion along selected
-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
-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 .edo
-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 implentation point of
view. Because parallel ED requires much extra communication, expect the
performance to be lower as in a free MD simulation, especially on a
large number of nodes.
All output of mdrun (specify with -eo) is written to a .edo file. In
the output file, per OUTFRQ step the following information is present:
* the step number
* the number of the ED dataset. (Note that you can impose multiple ED
constraints in a single simulation - on different molecules e.g. - if
several .edi files were concatenated first. The constraints are applied
in the order they appear in the .edi file.)
* RMSD (for atoms involved in fitting prior to calculating the ED
* projections of the positions onto selected eigenvectors
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
The origin is normally the average structure stored in the eigvec.trr
file. It can be changed with -ori to an arbitrary position in
configurational 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 alpha1. For restraining alpha1 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.
-f eigenvec.trr Input
Full precision trajectory: trr trj cpt
-eig eigenval.xvg Input, Opt.
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
-tar target.gro Input, Opt.
Structure file: gro g96 pdb tpr tpb tpa
-ori origin.gro Input, Opt.
Structure file: gro g96 pdb tpr tpb tpa
-o sam.edi Output
ED sampling input
Print help info and quit
-nice int 0
Set the nicelevel
Add specific codes (legends etc.) in the output xvg files for the
Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or
1-100:10 means 1 11 21 31 ... 91
Indices of eigenvectors for fixed increment linear sampling
Indices of eigenvectors for acceptance linear sampling
Indices of eigenvectors for flooding
Indices of eigenvectors for fixed increment radius expansion
Indices of eigenvectors for acceptance radius expansion
Indices of eigenvectors for acceptance radius contraction
-outfrq int 100
Freqency (in steps) of writing output in .edo file
-slope real 0
Minimal slope in acceptance radius expansion
-maxedsteps int 0
Max nr of steps per cycle
-deltaF0 real 150
Target destabilization energy - used for flooding
-deltaF real 0
Start deltaF with this parameter - default 0, i.e. 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
-eqsteps int 0
Number of steps to run without any perturbations
-Eflnull real 0
This is the starting value of the flooding strength. The flooding
strength is updated according to the adaptive flooding scheme. To use 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
Stepsizes (nm/step) for fixed increment linear sampling (put in
quotes! "1.0 2.3 5.1 -3.1")
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
Use the flooding potential with inverted sign - effects as
quasiharmonic restraining potential
The eigenvectors and eigenvalues are from a Hessian matrix
The eigenvalues are interpreted as spring constant
More information about GROMACS is available at
Thu 16 Oct 2008 make_edi(1)