--- /dev/null
+.TH g_densmap 1 "Mon 29 Aug 2005"
+.SH NAME
+g_densmap
+.B VERSION 3.3_beta_20050823
+.SH SYNOPSIS
+\f3g_densmap\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " densmap.xpm "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-bin" " real "
+.BI "-nx" " int "
+.BI "-nz" " int "
+.BI "-amax" " real "
+.BI "-rmax" " real "
+.BI "-[no]mirror" ""
+.BI "-dmax" " real "
+.SH DESCRIPTION
+g_densmap computes 2D number-density maps.
+It can make planar and axial-radial density maps.
+The output
+.B .xpm
+file can be visualized with for instance xv
+and can be converted to postscript with xpm2ps.
+
+
+
+The default analysis is a 2-D number-density map for a selected
+group of atoms in the x-z plane. The grid spacing is set with the option
+
+.B -bin
+. When
+.B -nx
+or
+.B -nz
+is non-zero, the grid
+size is set by this option. Box size fluctuations are properly taken
+into account.
+
+
+
+When options
+.B -amax
+and
+.B -rmax
+are set, an axial-radial
+number-density map is made. Three groups should be supplied, the centers
+of mass of the first two groups define the axis, the third defines the
+analysis group. The axial direction goes from -amax to +amax, where
+the center is defined as the midpoint between the centers of mass and
+the positive direction goes from the first to the second center of mass.
+The radial direction goes from 0 to rmax or from -rmax to +rmax
+when the
+.B -mirror
+option has been set.
+
+
+
+When you do not want the scale in the output to go
+from zero to the maximum density, you can set the maximum
+with the option
+.B -dmax
+.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Generic trajectory: xtc trr trj gro g96 pdb
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " densmap.xpm"
+.B Output
+ X PixMap compatible matrix file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0"
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-bin" " real" " 0.02"
+ Grid size
+
+.BI "-nx" " int" " 0"
+ Number of grid cells in x direction
+
+.BI "-nz" " int" " 0"
+ Number of grid cells in z direction
+
+.BI "-amax" " real" " 0"
+ Maximum axial distance from the center
+
+.BI "-rmax" " real" " 0"
+ Maximum radial distance
+
+.BI "-[no]mirror" " no"
+ Add the mirror image below the axial axis
+
+.BI "-dmax" " real" " 0"
+ Maximum density (0 means calculate it)
+
--- /dev/null
+.TH g_sham 1 "Mon 29 Aug 2005"
+.SH NAME
+g_sham
+.B VERSION 3.3_beta_20050823
+.SH SYNOPSIS
+\f3g_sham\fP
+.BI "-f" " graph.xvg "
+.BI "-ge" " gibbs.xvg "
+.BI "-ene" " esham.xvg "
+.BI "-dist" " ener.xvg "
+.BI "-histo" " edist.xvg "
+.BI "-bin" " bindex.ndx "
+.BI "-ls" " gibbs.xpm "
+.BI "-lsh" " enthalpy.xpm "
+.BI "-lss" " entropy.xpm "
+.BI "-map" " map.xpm "
+.BI "-ls3" " gibbs3.pdb "
+.BI "-mdata" " mapdata.xvg "
+.BI "-g" " shamlog.log "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-[no]time" ""
+.BI "-b" " real "
+.BI "-e" " real "
+.BI "-ttol" " real "
+.BI "-n" " int "
+.BI "-[no]d" ""
+.BI "-bw" " real "
+.BI "-[no]sham" ""
+.BI "-tsham" " real "
+.BI "-pmin" " real "
+.BI "-dim" " vector "
+.BI "-ngrid" " vector "
+.BI "-xmin" " vector "
+.BI "-xmax" " vector "
+.BI "-gmax" " real "
+.BI "-nlevels" " int "
+.BI "-mname" " string "
+.SH DESCRIPTION
+g_sham reads a number of xvg files and analyzes data sets.
+A line in the input file may start with a time
+(see option
+.B -time
+) and any number of y values may follow.
+Multiple sets can also be
+read when they are seperated by & (option
+.B -n
+),
+in this case only one y value is read from each line.
+All lines starting with and @ are skipped.
+
+
+
+Option
+.B -ge
+can be used to supply a file with free energies
+when the ensemble is not a Boltzmann ensemble, but has been biased
+by this free energy.
+
+
+
+With option
+.B -dim
+dimensions can be gives for distances.
+When a distance is 2- or 3-dimensional, the circumference or surface
+sampled by two particles increases with increasing distance.
+Depending on what one would like to show, one can choose to correct
+the free-energy for this volume effect.
+The probability is normalized by r and r2 for a dimension of 2 and 3
+respectively.
+Note that for angles between vectors the inner-product or cosine
+is the natural quantity to use, as it will produce bins of the same
+volume.
+.SH FILES
+.BI "-f" " graph.xvg"
+.B Input
+ xvgr/xmgr file
+
+.BI "-ge" " gibbs.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
+.BI "-ene" " esham.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
+.BI "-dist" " ener.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-histo" " edist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-bin" " bindex.ndx"
+.B Output, Opt.
+ Index file
+
+.BI "-ls" " gibbs.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-lsh" " enthalpy.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-lss" " entropy.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-map" " map.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-ls3" " gibbs3.pdb"
+.B Output, Opt.
+ Protein data bank file
+
+.BI "-mdata" " mapdata.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-g" " shamlog.log"
+.B Output, Opt.
+ Log file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-[no]w" " no"
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-[no]time" " yes"
+ Expect a time in the input
+
+.BI "-b" " real" " -1"
+ First time to read from set
+
+.BI "-e" " real" " -1"
+ Last time to read from set
+
+.BI "-ttol" " real" " 0"
+ Tolerance on time in appropriate units (usually ps)
+
+.BI "-n" " int" " 1"
+ Read sets seperated by &
+
+.BI "-[no]d" " no"
+ Use the derivative
+
+.BI "-bw" " real" " 0.1"
+ Binwidth for the distribution
+
+.BI "-[no]sham" " yes"
+ Turn off energy weighting even if energies are given
+
+.BI "-tsham" " real" " 298.15"
+ Temperature for single histogram analysis
+
+.BI "-pmin" " real" " 0"
+ Minimum probability. Anything lower than this will be set to zero
+
+.BI "-dim" " vector" " 1 1 1"
+ Dimensions for distances, used for volume correction (max 3 values, dimensions 3 will get the same value as the last)
+
+.BI "-ngrid" " vector" " 32 32 32"
+ Number of bins for energy landscapes (max 3 values, dimensions 3 will get the same value as the last)
+
+.BI "-xmin" " vector" " 0 0 0"
+ Minimum for the axes in energy landscape (see above for 3 dimensions)
+
+.BI "-xmax" " vector" " 1 1 1"
+ Maximum for the axes in energy landscape (see above for 3 dimensions)
+
+.BI "-gmax" " real" " 0"
+ Maximum level in output, 0 is calculate
+
+.BI "-nlevels" " int" " 25"
+ Number of levels for energy landscape from single histogram analysis
+
+.BI "-mname" " string" " "
+ Legend label for the custom landscape
+
--- /dev/null
+.TH make_edi 1 "Mon 29 Aug 2005"
+.SH NAME
+make_edi
+.B VERSION 3.3_beta_20050823
+.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 "-nice" " int "
+.BI "-[no]xvgr" ""
+.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 "-logfrq" " int "
+.BI "-slope" " real "
+.BI "-maxedsteps" " int "
+.BI "-deltaF0" " real "
+.BI "-deltaF" " real "
+.BI "-tau" " real "
+.BI "-eqsteps" " int "
+.BI "-Eflnull" " real "
+.BI "-T" " real "
+.BI "-alpha" " real "
+.BI "-linstep" " string "
+.BI "-accdir" " string "
+.BI "-radstep" " real "
+.BI "-[no]restrain" ""
+.BI "-[no]hesse" ""
+.BI "-[no]harmonic" ""
+.SH DESCRIPTION
+
+.B make_edi
+generates an ED-sampling input file to be used with mdrun
+based on eigenvectors of a covariance matrix (
+.B g_covar
+) or from a
+Normal Modes anaysis (
+.B 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
+(
+.B -linfix
+,
+.B -linacc
+,
+.B -radfix
+,
+.B -radacc
+,
+.B -radcon
+),
+to keep the position along a certain (set of) coordinate(s) fixed (
+.B -linfix
+),
+or to only monitor the projections of the positions, velocities and forces onto
+these coordinates(
+.B -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.
+
+
+
+.B -mon
+: monitor projections of x, v and f onto selected eigenvectors.
+
+
+
+.B -linfix
+: perform fixed-step linear expansion along selected eigenvectors.
+
+
+
+.B -linacc
+: perform acceptance linear expansion along selected eigenvectors.
+(steps in the desired directions will be accepted, others will be rejected).
+
+
+
+.B -radfix
+: perform fixed-step radius expansion along selected eigenvectors.
+
+
+
+.B -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
+.B -ori
+is specified, you will be able
+to read in a structure file that defines an external origin.
+
+
+.B -radcon
+: perform acceptance radius contraction along selected eigenvectors
+towards a target structure specified with
+.B -tar
+.NOTE: each eigenvector can be selected only once.
+
+
+.B -outfrq
+: frequency (in steps) of writing out projections etc.
+
+
+
+.B -logfrq
+: frequency (in steps) of writing out statistics to log file.
+
+
+
+.B -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.
+
+
+.B -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 (it would
+require much extra communication to fully parallelize the algorithms).
+Fortunately, however, a typical parallel protein simulation in gromacs has
+most or all protein coordinates on one processor (the master) and has only
+other atoms (solvent, lipid, ions etc) on the other processors. With such a
+setup, ED sampling will still work. If the atoms over which ED sampling should
+be performed are spread over multiple processors, a fatal error will result.
+
+All output of mdrun (specify with -eo) is written to a .edo file (some extra
+information is written to the log file of mdrun too, actually). The .edo format
+is a simple ASCII file that should be easy to parse with standard unix tools
+like awk. A script (parse_edo) can be downloaded from contribution section at
+ www.gromacs.org to extract information from the
+.edo files for your convinience. In short, the header defines which information
+can be expected in the rest of the .edo file. After the header, per step the
+following information is present:
+
+
+* the step number
+
+* RMSD (for atoms in fitting prior to calculating ED constr.)
+
+* projections of the positions onto selected eigenvectors
+
+* projections of the velocities onto selected eigenvectors
+
+* projections of the forces onto selected eigenvectors
+
+
+
+All projections are in the same order as in the header, so if you have e.g.
+2 groups (say one group over which acceptance radius expansion is performed,
+and another for which the projections are merely monitored) then you first
+get the position projections for each of the 2 groups, then the velocities
+and then the forces. Radii are not explicitly written to the .edo file, as
+they can be readily projected back from the positions. Alternatively, radii
+may be 'grepped from the log file.
+
+
+
+
+
+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 configurational space
+with -tau , -deltaF0 and -Eflnull you control the flooding strength
+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 alpha1for restraining alpha1 can give you smaller width in the restraining potentialRESTART and FLOODING:
+If you want to restart a crashed flooding simulation please find the values deltaF and Efl in
+the output file and write them with your texteditor into the .edi file under DELTA_F0 and EFL_NULL
+.SH FILES
+.BI "-f" " eigenvec.trr"
+.B Input
+ Full precision trajectory: trr trj
+
+.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 xml
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-tar" " target.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa xml
+
+.BI "-ori" " origin.gro"
+.B Input, Opt.
+ Generic structure: gro g96 pdb tpr tpb tpa xml
+
+.BI "-o" " sam.edi"
+.B Output
+ ED sampling input
+
+.SH OTHER OPTIONS
+.BI "-[no]h" " no"
+ Print help info and quit
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]xvgr" " yes"
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-mon" " string" " "
+ Indices of eigenvectors for projections of x, v and f (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 .edo file
+
+.BI "-logfrq" " int" " 100"
+ frequency (in steps) of writing to log
+
+.BI "-slope" " real" " 0"
+ minimal slope in acceptance radius expamsion
+
+.BI "-maxedsteps" " int" " 0"
+ max nr of steps per cycle
+
+.BI "-deltaF0" " real" " 150"
+ target destabilization energy - used for flooding
+
+.BI "-deltaF" " real" " 0"
+ start deltaF with this parameter - default 0, i.g. 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 "-eqsteps" " int" " 0"
+ number of steps to run without any perturbations
+
+.BI "-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.
+
+.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 "-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 "-[no]restrain" " no"
+ use the flooding potential with inverted sign - effects as quasiharmonic restraining potential
+
+.BI "-[no]hesse" " no"
+ the eigenvectors and eigenvalues are from a Hesse matrix
+
+.BI "-[no]harmonic" " no"
+ the eigenvalues are interpreted as spring constant
+
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff