.TH make_edi 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME make_edi - generate input files for essential dynamics sampling .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3make_edi\fP .BI "\-f" " eigenvec.trr " .BI "\-eig" " eigenval.xvg " .BI "\-s" " topol.tpr " .BI "\-n" " index.ndx " .BI "\-tar" " target.gro " .BI "\-ori" " origin.gro " .BI "\-o" " sam.edi " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-xvg" " enum " .BI "\-mon" " string " .BI "\-linfix" " string " .BI "\-linacc" " string " .BI "\-radfix" " string " .BI "\-radacc" " string " .BI "\-radcon" " string " .BI "\-flood" " string " .BI "\-outfrq" " int " .BI "\-slope" " real " .BI "\-linstep" " string " .BI "\-accdir" " string " .BI "\-radstep" " real " .BI "\-maxedsteps" " int " .BI "\-eqsteps" " int " .BI "\-deltaF0" " real " .BI "\-deltaF" " real " .BI "\-tau" " real " .BI "\-Eflnull" " real " .BI "\-T" " real " .BI "\-alpha" " real " .BI "\-[no]restrain" "" .BI "\-[no]hessian" "" .BI "\-[no]harmonic" "" .BI "\-constF" " string " .SH DESCRIPTION \&\fB make_edi\fR generates an essential dynamics (ED) sampling input file to be used with \fB mdrun\fR \&based on eigenvectors of a covariance matrix (\fB g_covar\fR) or from a \&normal modes anaysis (\fB g_nmeig\fR). \&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 \&(\fB \-linfix\fR, \fB \-linacc\fR, \fB \-radfix\fR, \fB \-radacc\fR, \fB \-radcon\fR), \&to keep the position along a certain (set of) coordinate(s) fixed (\fB \-linfix\fR), \&or to only monitor the projections of the positions onto \&these coordinates (\fB \-mon\fR). \&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. \&\fB \-mon\fR: monitor projections of the coordinates onto selected eigenvectors. \&\fB \-linfix\fR: perform fixed\-step linear expansion along selected eigenvectors. \&\fB \-linacc\fR: perform acceptance linear expansion along selected eigenvectors. \&(steps in the desired directions will be accepted, others will be rejected). \&\fB \-radfix\fR: perform fixed\-step radius expansion along selected eigenvectors. \&\fB \-radacc\fR: perform acceptance radius expansion along selected eigenvectors. \&(steps in the desired direction will be accepted, others will be rejected). \&\fB Note:\fR by default the starting MD structure will be taken as origin of the first \&expansion cycle for radius expansion. If \fB \-ori\fR is specified, you will be able \&to read in a structure file that defines an external origin. \&\fB \-radcon\fR: perform acceptance radius contraction along selected eigenvectors \&towards a target structure specified with \fB \-tar\fR. \&NOTE: each eigenvector can be selected only once. \&\fB \-outfrq\fR: frequency (in steps) of writing out projections etc. to \fB .edo\fR file \&\fB \-slope\fR: 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. \&\fB \-maxedsteps\fR: 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 \¶llel ED requires some extra communication, expect the performance to be \&lower as in a free MD simulation, especially on a large number of nodes. \&All output of \fB mdrun\fR (specify with \fB \-eo\fR) is written to a .edo file. In the output \&file, per OUTFRQ step the following information is present: \&\fB *\fR the step number \&\fB *\fR the number of the ED dataset. (\fB Note\fR that you can impose multiple ED constraints in \&a single simulation (on different molecules) if several \fB .edi\fR files were concatenated \&first. The constraints are applied in the order they appear in the \fB .edi\fR file.) \&\fB *\fR RMSD (for atoms involved in fitting prior to calculating the ED constraints) \&* projections of the positions onto selected eigenvectors \& \&FLOODING: \&with \fB \-flood\fR, 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 \fB eigvec.trr\fR file. \&It can be changed with \fB \-ori\fR to an arbitrary position in configurational space. \&With \fB \-tau\fR, \fB \-deltaF0\fR, and \fB \-Eflnull\fR 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 \fB \-tau\fR to zero. \& \&\fB \-alpha\fR 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 \fB .edi\fR file under DELTA_F0 and EFL_NULL. .SH FILES .BI "\-f" " eigenvec.trr" .B Input Full precision trajectory: trr trj cpt .BI "\-eig" " eigenval.xvg" .B Input, Opt. xvgr/xmgr file .BI "\-s" " topol.tpr" .B Input Structure+mass(db): tpr tpb tpa gro g96 pdb .BI "\-n" " index.ndx" .B Input, Opt. Index file .BI "\-tar" " target.gro" .B Input, Opt. Structure file: gro g96 pdb tpr etc. .BI "\-ori" " origin.gro" .B Input, Opt. Structure file: gro g96 pdb tpr etc. .BI "\-o" " sam.edi" .B Output ED sampling input .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-xvg" " enum" " xmgrace" xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR .BI "\-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 .BI "\-linfix" " string" " " Indices of eigenvectors for fixed increment linear sampling .BI "\-linacc" " string" " " Indices of eigenvectors for acceptance linear sampling .BI "\-radfix" " string" " " Indices of eigenvectors for fixed increment radius expansion .BI "\-radacc" " string" " " Indices of eigenvectors for acceptance radius expansion .BI "\-radcon" " string" " " Indices of eigenvectors for acceptance radius contraction .BI "\-flood" " string" " " Indices of eigenvectors for flooding .BI "\-outfrq" " int" " 100" Freqency (in steps) of writing output in \fB .edo\fR file .BI "\-slope" " real" " 0 " Minimal slope in acceptance radius expansion .BI "\-linstep" " string" " " Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 \-3.1") .BI "\-accdir" " string" " " Directions for acceptance linear sampling \- only sign counts! (put in quotes! "\-1 +1 \-1.1") .BI "\-radstep" " real" " 0 " Stepsize (nm/step) for fixed increment radius expansion .BI "\-maxedsteps" " int" " 0" Maximum number of steps per cycle .BI "\-eqsteps" " int" " 0" Number of steps to run without any perturbations .BI "\-deltaF0" " real" " 150 " Target destabilization energy for flooding .BI "\-deltaF" " real" " 0 " Start deltaF with this parameter \- default 0, nonzero values only needed for restart .BI "\-tau" " real" " 0.1 " Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength .BI "\-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 \fB \-tau\fR 0. .BI "\-T" " real" " 300 " T is temperature, the value is needed if you want to do flooding .BI "\-alpha" " real" " 1 " Scale width of gaussian flooding potential with alpha2 .BI "\-[no]restrain" "no " Use the flooding potential with inverted sign \- effects as quasiharmonic restraining potential .BI "\-[no]hessian" "no " The eigenvectors and eigenvalues are from a Hessian matrix .BI "\-[no]harmonic" "no " The eigenvalues are interpreted as spring constant .BI "\-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. .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.