1make_edi(1) GROMACS suite, VERSION 4.5 make_edi(1)
2
6 make_edi - generate input files for essential dynamics sampling
7 VERSION 4.5
9
11 make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -n index.ndx
12 -tar target.gro -ori origin.gro -o sam.edi -[no]h -[no]version -nice
13 int -xvg enum -mon string -linfix string -linacc string -flood string
14 -radfix string -radacc string -radcon string -outfrq int -slope real
15 -maxedsteps int -deltaF0 real -deltaF real -tau real -eqsteps int
16 -Eflnull real -T real -alpha real -linstep string -accdir string -rad‐
17 step real -[no]restrain -[no]hessian -[no]harmonic
18
20 make_edi generates an essential dynamics (ED) sampling input file to
21 be used with mdrun based on eigenvectors of a covariance matrix (
22 g_covar) or from a normal modes anaysis ( g_nmeig). ED sampling can be
23 used to manipulate the position along collective coordinates (eigenvec‐
24 tors) of (biological) macromolecules during a simulation. Particularly,
25 it may be used to enhance the sampling efficiency of MD simulations by
26 stimulating the system to explore new regions along these collective
27 coordinates. A number of different algorithms are implemented to drive
28 the system along the eigenvectors ( -linfix, -linacc, -radfix,
29 -radacc, -radcon), to keep the position along a certain (set of) coor‐
30 dinate(s) fixed ( -linfix), or to only monitor the projections of the
31 positions onto these coordinates ( -mon).
32 References:
35 A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and H.J.C.
37 Berendsen; An efficient method for sampling the essential subspace of
38 proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)
39 B.L. de Groot, A. Amadei, D.M.F. van Aalten and H.J.C. Berendsen;
41 Towards an exhaustive sampling of the configurational spaces of the two
42 forms of the peptide hormone guanylin, J. Biomol. Struct. Dyn. 13 :
43 741-751 (1996)
44 B.L. de Groot, A.Amadei, R.M. Scheek, N.A.J. van Nuland and H.J.C.
46 Berendsen; An extended sampling of the configurational space of HPr
47 from E. coli PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996)
48 You will be prompted for one or more index groups that correspond to
50 the eigenvectors, reference structure, target positions, etc.
51 -mon: monitor projections of the coordinates onto selected eigenvec‐
54 tors.
55 -linfix: perform fixed-step linear expansion along selected eigenvec‐
58 tors.
59 -linacc: perform acceptance linear expansion along selected eigenvec‐
62 tors. (steps in the desired directions will be accepted, others will
63 be rejected).
64 -radfix: perform fixed-step radius expansion along selected eigenvec‐
67 tors.
68 -radacc: perform acceptance radius expansion along selected eigenvec‐
71 tors. (steps in the desired direction will be accepted, others will be
72 rejected). Note: by default the starting MD structure will be taken as
73 origin of the first expansion cycle for radius expansion. If -ori is
74 specified, you will be able to read in a structure file that defines an
75 external origin.
76 -radcon: perform acceptance radius contraction along selected eigen‐
79 vectors towards a target structure specified with -tar.
80 NOTE: each eigenvector can be selected only once.
83 -outfrq: frequency (in steps) of writing out projections etc. to .edo
86 file
87 -slope: minimal slope in acceptance radius expansion. A new expansion
90 cycle will be started if the spontaneous increase of the radius (in
91 nm/step) is less than the value specified.
92 -maxedsteps: maximum number of steps per cycle in radius expansion
95 before a new cycle is started.
96 Note on the parallel implementation: since ED sampling is a 'global'
99 thing (collective coordinates etc.), at least on the 'protein' side, ED
100 sampling is not very parallel-friendly from an implentation point of
101 view. Because parallel ED requires much extra communication, expect the
102 performance to be lower as in a free MD simulation, especially on a
103 large number of nodes.
104 All output of mdrun (specify with -eo) is written to a .edo file. In
107 the output file, per OUTFRQ step the following information is present:
108 * the step number
111 * the number of the ED dataset. (Note that you can impose multiple ED
113 constraints in a single simulation - on different molecules e.g. - if
114 several .edi files were concatenated first. The constraints are applied
115 in the order they appear in the .edi file.)
116 * RMSD (for atoms involved in fitting prior to calculating the ED con‐
118 straints)
119 * projections of the positions onto selected eigenvectors
121 FLOODING:
128 with -flood you can specify which eigenvectors are used to compute a
131 flooding potential, which will lead to extra forces expelling the
132 structure out of the region described by the covariance matrix. If you
133 switch -restrain the potential is inverted and the structure is kept in
134 that region.
135 The origin is normally the average structure stored in the eigvec.trr
138 file. It can be changed with -ori to an arbitrary position in configu‐
139 rational space. With -tau, -deltaF0 and -Eflnull you control the
140 flooding behaviour. Efl is the flooding strength, it is updated
141 according to the rule of adaptive flooding. Tau is the time constant
142 of adaptive flooding, high tau means slow adaption (i.e. growth).
143 DeltaF0 is the flooding strength you want to reach after tau ps of sim‐
144 ulation. To use constant Efl set -tau to zero.
145 -alpha is a fudge parameter to control the width of the flooding poten‐
148 tial. A value of 2 has been found to give good results for most stan‐
149 dard cases in flooding of proteins. Alpha basically accounts for
150 incomplete sampling, if you sampled further the width of the ensemble
151 would increase, this is mimicked by alpha1. For restraining alpha1 can
152 give you smaller width in the restraining potential.
153 RESTART and FLOODING: If you want to restart a crashed flooding simula‐
156 tion please find the values deltaF and Efl in the output file and manu‐
157 ally put them into the .edi file under DELTA_F0 and EFL_NULL.
158
160 -f eigenvec.trr Input
161 Full precision trajectory: trr trj cpt
162 -eig eigenval.xvg Input, Opt.
164 xvgr/xmgr file
165 -s topol.tpr Input
167 Structure+mass(db): tpr tpb tpa gro g96 pdb
168 -n index.ndx Input, Opt.
170 Index file
171 -tar target.gro Input, Opt.
173 Structure file: gro g96 pdb tpr etc.
174 -ori origin.gro Input, Opt.
176 Structure file: gro g96 pdb tpr etc.
177 -o sam.edi Output
179 ED sampling input
180
183 -[no]hno
184 Print help info and quit
185 -[no]versionno
187 Print version info and quit
188 -nice int 0
190 Set the nicelevel
191 -xvg enum xmgrace
193 xvg plot formatting: xmgrace, xmgr or none
194 -mon string
196 Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or
197 1-100:10 means 1 11 21 31 ... 91
198 -linfix string
200 Indices of eigenvectors for fixed increment linear sampling
201 -linacc string
203 Indices of eigenvectors for acceptance linear sampling
204 -flood string
206 Indices of eigenvectors for flooding
207 -radfix string
209 Indices of eigenvectors for fixed increment radius expansion
210 -radacc string
212 Indices of eigenvectors for acceptance radius expansion
213 -radcon string
215 Indices of eigenvectors for acceptance radius contraction
216 -outfrq int 100
218 Freqency (in steps) of writing output in .edo file
219 -slope real 0
221 Minimal slope in acceptance radius expansion
222 -maxedsteps int 0
224 Max nr of steps per cycle
225 -deltaF0 real 150
227 Target destabilization energy - used for flooding
228 -deltaF real 0
230 Start deltaF with this parameter - default 0, i.e. nonzero values only
231 needed for restart
232 -tau real 0.1
234 Coupling constant for adaption of flooding strength according to
235 deltaF0, 0 = infinity i.e. constant flooding strength
236 -eqsteps int 0
238 Number of steps to run without any perturbations
239 -Eflnull real 0
241 This is the starting value of the flooding strength. The flooding
242 strength is updated according to the adaptive flooding scheme. To use a
243 constant flooding strength use -tau 0.
244 -T real 300
246 T is temperature, the value is needed if you want to do flooding
247 -alpha real 1
249 Scale width of gaussian flooding potential with alpha2
250 -linstep string
252 Stepsizes (nm/step) for fixed increment linear sampling (put in
253 quotes! "1.0 2.3 5.1 -3.1")
254 -accdir string
256 Directions for acceptance linear sampling - only sign counts! (put in
257 quotes! "-1 +1 -1.1")
258 -radstep real 0
260 Stepsize (nm/step) for fixed increment radius expansion
261 -[no]restrainno
263 Use the flooding potential with inverted sign - effects as quasihar‐
264 monic restraining potential
265 -[no]hessianno
267 The eigenvectors and eigenvalues are from a Hessian matrix
268 -[no]harmonicno
270 The eigenvalues are interpreted as spring constant
271
274 gromacs(7)
275 More information about GROMACS is available at <http://www.gro‐
277 macs.org/>.
278 Thu 26 Aug 2010 make_edi(1)