1GMX-MAKE_EDI(1)                     GROMACS                    GMX-MAKE_EDI(1)
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NAME

6       gmx-make_edi - Generate input files for essential dynamics sampling
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SYNOPSIS

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

23       gmx  make_edi  generates an essential dynamics (ED) sampling input file
24       to be used with mdrun based on eigenvectors of a covariance matrix (gmx
25       covar) or from a normal modes analysis (gmx nmeig).  ED sampling can be
26       used to manipulate the position along collective coordinates (eigenvec‐
27       tors) of (biological) macromolecules during a simulation. Particularly,
28       it may be used to enhance the sampling efficiency of MD simulations  by
29       stimulating  the  system  to explore new regions along these collective
30       coordinates. A number of different algorithms are implemented to  drive
31       the  system along the eigenvectors (-linfix, -linacc, -radfix, -radacc,
32       -radcon), to keep the position along a certain (set  of)  coordinate(s)
33       fixed  (-linfix),  or  to only monitor the projections of the positions
34       onto these coordinates (-mon).
35
36       References:
37
38       A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and  H.J.C.
39       Berendsen;  An  efficient method for sampling the essential subspace of
40       proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)
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42       B.L. de Groot, A. Amadei,  D.M.F.  van  Aalten  and  H.J.C.  Berendsen;
43       Towards an exhaustive sampling of the configurational spaces of the two
44       forms of the peptide hormone guanylin, J. Biomol.  Struct.  Dyn.  13  :
45       741-751 (1996)
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47       B.L.  de  Groot,  A.Amadei,  R.M.  Scheek, N.A.J. van Nuland and H.J.C.
48       Berendsen; An extended sampling of the  configurational  space  of  HPr
49       from E. coli Proteins: Struct. Funct. Gen. 26: 314-322 (1996)
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51       You  will  be  prompted for one or more index groups that correspond to
52       the eigenvectors, reference structure, target positions, etc.
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54       -mon: monitor projections of the coordinates  onto  selected  eigenvec‐
55       tors.
56
57       -linfix:  perform  fixed-step linear expansion along selected eigenvec‐
58       tors.
59
60       -linacc: perform acceptance linear expansion along  selected  eigenvec‐
61       tors.   (steps  in the desired directions will be accepted, others will
62       be rejected).
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64       -radfix: perform fixed-step radius expansion along  selected  eigenvec‐
65       tors.
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67       -radacc:  perform  acceptance radius expansion along selected eigenvec‐
68       tors.  (steps in the desired direction will be accepted, others will be
69       rejected).  Note: by default the starting MD structure will be taken as
70       origin of the first expansion cycle for radius expansion.  If  -ori  is
71       specified, you will be able to read in a structure file that defines an
72       external origin.
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74       -radcon: perform acceptance radius contraction along selected eigenvec‐
75       tors towards a target structure specified with -tar.
76
77       NOTE: each eigenvector can be selected only once.
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79       -outfrq:  frequency  (in steps) of writing out projections etc. to .xvg
80       file
81
82       -slope: minimal slope in acceptance radius expansion. A  new  expansion
83       cycle  will  be  started  if the spontaneous increase of the radius (in
84       nm/step) is less than the value specified.
85
86       -maxedsteps: maximum number of steps  per  cycle  in  radius  expansion
87       before a new cycle is started.
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89       Note  on  the  parallel implementation: since ED sampling is a ‘global’
90       thing (collective coordinates etc.), at least on the ‘protein’ side, ED
91       sampling  is not very parallel-friendly from an implementation point of
92       view. Because parallel ED requires some extra communication, expect the
93       performance  to  be  lower  as in a free MD simulation, especially on a
94       large number of ranks and/or when the ED group contains a lot of atoms.
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96       Please also note that if your ED group contains more than a single pro‐
97       tein, then the .tpr file must contain the correct PBC representation of
98       the ED group.  Take a look on  the  initial  RMSD  from  the  reference
99       structure, which is printed out at the start of the simulation; if this
100       is much higher than expected, one of the ED molecules might be  shifted
101       by a box vector.
102
103       All  ED-related output of mdrun (specify with -eo) is written to a .xvg
104       file as a function of time in intervals of OUTFRQ steps.
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106       Note that you can impose multiple ED constraints  and  flooding  poten‐
107       tials  in  a single simulation (on different molecules) if several .edi
108       files were concatenated first. The constraints are applied in the order
109       they  appear  in the .edi file.  Depending on what was specified in the
110       .edi input file, the output file contains for each ED dataset
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112          · the RMSD of the fitted molecule to the  reference  structure  (for
113            atoms involved in fitting prior to calculating the ED constraints)
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115          · projections of the positions onto selected eigenvectors
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117       FLOODING:
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119       with  -flood,  you can specify which eigenvectors are used to compute a
120       flooding potential, which will  lead  to  extra  forces  expelling  the
121       structure  out of the region described by the covariance matrix. If you
122       switch -restrain the potential is inverted and the structure is kept in
123       that region.
124
125       The  origin  is normally the average structure stored in the eigvec.trr
126       file.  It can be changed with -ori to an arbitrary position in configu‐
127       ration space.  With -tau, -deltaF0, and -Eflnull you control the flood‐
128       ing behaviour.  Efl is the flooding strength, it is  updated  according
129       to the rule of adaptive flooding.  Tau is the time constant of adaptive
130       flooding, high tau means slow adaption (i.e. growth).  DeltaF0  is  the
131       flooding strength you want to reach after tau ps of simulation.  To use
132       constant Efl set -tau to zero.
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134       -alpha is a fudge parameter to control the width of the flooding poten‐
135       tial.  A  value of 2 has been found to give good results for most stan‐
136       dard cases in flooding  of  proteins.   alpha  basically  accounts  for
137       incomplete  sampling,  if you sampled further the width of the ensemble
138       would increase, this is mimicked by alpha > 1.  For restraining,  alpha
139       < 1 can give you smaller width in the restraining potential.
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141       RESTART and FLOODING: If you want to restart a crashed flooding simula‐
142       tion please find the values deltaF and Efl in the output file and manu‐
143       ally put them into the .edi file under DELTA_F0 and EFL_NULL.
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OPTIONS

146       Options to specify input files:
147
148       -f [<.trr/.cpt/…>] (eigenvec.trr)
149              Full precision trajectory: trr cpt tng
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151       -eig [<.xvg>] (eigenval.xvg) (Optional)
152              xvgr/xmgr file
153
154       -s [<.tpr/.gro/…>] (topol.tpr)
155              Structure+mass(db): tpr gro g96 pdb brk ent
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157       -n [<.ndx>] (index.ndx) (Optional)
158              Index file
159
160       -tar [<.gro/.g96/…>] (target.gro) (Optional)
161              Structure file: gro g96 pdb brk ent esp tpr
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163       -ori [<.gro/.g96/…>] (origin.gro) (Optional)
164              Structure file: gro g96 pdb brk ent esp tpr
165
166       Options to specify output files:
167
168       -o [<.edi>] (sam.edi)
169              ED sampling input
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171       Other options:
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173       -xvg <enum> (xmgrace)
174              xvg plot formatting: xmgrace, xmgr, none
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176       -mon <string>
177              Indices  of  eigenvectors for projections of x (e.g. 1,2-5,9) or
178              1-100:10 means 1 11 21 31 … 91
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180       -linfix <string>
181              Indices of eigenvectors for fixed increment linear sampling
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183       -linacc <string>
184              Indices of eigenvectors for acceptance linear sampling
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186       -radfix <string>
187              Indices of eigenvectors for fixed increment radius expansion
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189       -radacc <string>
190              Indices of eigenvectors for acceptance radius expansion
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192       -radcon <string>
193              Indices of eigenvectors for acceptance radius contraction
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195       -flood <string>
196              Indices of eigenvectors for flooding
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198       -outfrq <int> (100)
199              Frequency (in steps) of writing output in .xvg file
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201       -slope <real> (0)
202              Minimal slope in acceptance radius expansion
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204       -linstep <string>
205              Stepsizes (nm/step) for fixed increment linear sampling (put  in
206              quotes! “1.0 2.3 5.1 -3.1”)
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208       -accdir <string>
209              Directions  for  acceptance  linear sampling - only sign counts!
210              (put in quotes! “-1 +1 -1.1”)
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212       -radstep <real> (0)
213              Stepsize (nm/step) for fixed increment radius expansion
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215       -maxedsteps <int> (0)
216              Maximum number of steps per cycle
217
218       -eqsteps <int> (0)
219              Number of steps to run without any perturbations
220
221       -deltaF0 <real> (150)
222              Target destabilization energy for flooding
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224       -deltaF <real> (0)
225              Start deltaF with this parameter -  default  0,  nonzero  values
226              only needed for restart
227
228       -tau <real> (0.1)
229              Coupling constant for adaption of flooding strength according to
230              deltaF0, 0 = infinity i.e. constant flooding strength
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232       -Eflnull <real> (0)
233              The starting  value  of  the  flooding  strength.  The  flooding
234              strength  is  updated according to the adaptive flooding scheme.
235              For a constant flooding strength use -tau 0.
236
237       -T <real> (300)
238              T is temperature, the value is needed if you want to do flooding
239
240       -alpha <real> (1)
241              Scale width of gaussian flooding potential with alpha^2
242
243       -[no]restrain (no)
244              Use the flooding potential with  inverted  sign  ->  effects  as
245              quasiharmonic restraining potential
246
247       -[no]hessian (no)
248              The eigenvectors and eigenvalues are from a Hessian matrix
249
250       -[no]harmonic (no)
251              The eigenvalues are interpreted as spring constant
252
253       -constF <string>
254              Constant  force flooding: manually set the forces for the eigen‐
255              vectors selected with  -flood  (put  in  quotes!  “1.0  2.3  5.1
256              -3.1”).  No other flooding parameters are needed when specifying
257              the forces directly.
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SEE ALSO

260       gmx(1)
261
262       More    information    about    GROMACS    is    available    at     <‐
263       http://www.gromacs.org/>.
264
266       2020, GROMACS development team
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2712019.6                           Feb 28, 2020                  GMX-MAKE_EDI(1)
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