gmx sham¶
Synopsis¶
gmx sham [-f [<.xvg>]] [-ge [<.xvg>]] [-ene [<.xvg>]] [-dist [<.xvg>]] [-histo [<.xvg>]] [-bin [<.ndx>]] [-lp [<.xpm>]] [-ls [<.xpm>]] [-lsh [<.xpm>]] [-lss [<.xpm>]] [-ls3 [<.pdb>]] [-g [<.log>]] [-[no]w] [-xvg <enum>] [-[no]time] [-b <real>] [-e <real>] [-ttol <real>] [-n <int>] [-[no]d] [-[no]sham] [-tsham <real>] [-pmin <real>] [-dim <vector>] [-ngrid <vector>] [-xmin <vector>] [-xmax <vector>] [-pmax <real>] [-gmax <real>] [-emin <real>] [-emax <real>] [-nlevels <int>]
Description¶
gmx sham
makes multi-dimensional free-energy, enthalpy and entropy plots.
gmx sham
reads one or more .xvg files and analyzes data sets.
The basic purpose of gmx sham
is to plot Gibbs free energy landscapes
(option -ls
)
by Bolzmann inverting multi-dimensional histograms (option -lp
),
but it can also
make enthalpy (option -lsh
) and entropy (option -lss
)
plots. The histograms can be made for any quantities the user supplies.
A line in the input file may start with a time
(see option -time
) and any number of y-values may follow.
Multiple sets can also be
read when they are separated by & (option -n
),
in this case only one y-value is read from each line.
All lines starting with # and @ are skipped.
Option -ge
can be used to supply a file with free energies
when the ensemble is not a Boltzmann ensemble, but needs to be biased
by this free energy. One free energy value is required for each
(multi-dimensional) data point in the -f
input.
Option -ene
can be used to supply a file with energies.
These energies are used as a weighting function in the single
histogram analysis method by Kumar et al. When temperatures
are supplied (as a second column in the file), an experimental
weighting scheme is applied. In addition the vales
are used for making enthalpy and entropy plots.
With option -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 histogram and free-energy for this volume effect.
The probability is normalized by r and r^2 for dimensions of 2 and 3,
respectively.
A value of -1 is used to indicate an angle in degrees between two
vectors: a sin(angle) normalization will be applied.
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.
Options¶
Options to specify input files:
-f
[<.xvg>] (graph.xvg)- xvgr/xmgr file
-ge
[<.xvg>] (gibbs.xvg) (Optional)- xvgr/xmgr file
-ene
[<.xvg>] (esham.xvg) (Optional)- xvgr/xmgr file
Options to specify output files:
-dist
[<.xvg>] (ener.xvg) (Optional)- xvgr/xmgr file
-histo
[<.xvg>] (edist.xvg) (Optional)- xvgr/xmgr file
-bin
[<.ndx>] (bindex.ndx) (Optional)- Index file
-lp
[<.xpm>] (prob.xpm) (Optional)- X PixMap compatible matrix file
-ls
[<.xpm>] (gibbs.xpm) (Optional)- X PixMap compatible matrix file
-lsh
[<.xpm>] (enthalpy.xpm) (Optional)- X PixMap compatible matrix file
-lss
[<.xpm>] (entropy.xpm) (Optional)- X PixMap compatible matrix file
-ls3
[<.pdb>] (gibbs3.pdb) (Optional)- Protein data bank file
-g
[<.log>] (shamlog.log) (Optional)- Log file
Other options:
-[no]w
(no)- View output .xvg, .xpm, .eps and .pdb files
-xvg
<enum> (xmgrace)- xvg plot formatting: xmgrace, xmgr, none
-[no]time
(yes)- Expect a time in the input
-b
<real> (-1)- First time to read from set
-e
<real> (-1)- Last time to read from set
-ttol
<real> (0)- Tolerance on time in appropriate units (usually ps)
-n
<int> (1)- Read this number of sets separated by lines containing only an ampersand
-[no]d
(no)- Use the derivative
-[no]sham
(yes)- Turn off energy weighting even if energies are given
-tsham
<real> (298.15)- Temperature for single histogram analysis
-pmin
<real> (0)- Minimum probability. Anything lower than this will be set to zero
-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)
-ngrid
<vector> (32 32 32)- Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)
-xmin
<vector> (0 0 0)- Minimum for the axes in energy landscape (see above for > 3 dimensions)
-xmax
<vector> (1 1 1)- Maximum for the axes in energy landscape (see above for > 3 dimensions)
-pmax
<real> (0)- Maximum probability in output, default is calculate
-gmax
<real> (0)- Maximum free energy in output, default is calculate
-emin
<real> (0)- Minimum enthalpy in output, default is calculate
-emax
<real> (0)- Maximum enthalpy in output, default is calculate
-nlevels
<int> (25)- Number of levels for energy landscape