# g_sham_d (1) - Linux Manuals

## g_sham_d: read/write xmgr and xvgr data sets

## NAME

g_sham - read/write xmgr and xvgr data sets## SYNOPSIS

**g_sham**

**-f**

*graph.xvg*

**-ge**

*gibbs.xvg*

**-ene**

*esham.xvg*

**-dist**

*ener.xvg*

**-histo**

*edist.xvg*

**-bin**

*bindex.ndx*

**-lp**

*prob.xpm*

**-ls**

*gibbs.xpm*

**-lsh**

*enthalpy.xpm*

**-lss**

*entropy.xpm*

**-map**

*map.xpm*

**-ls3**

*gibbs3.pdb*

**-mdata**

*mapdata.xvg*

**-g**

*shamlog.log*

**-[no]h**

**-nice**

*int*

**-[no]w**

**-[no]xvgr**

**-[no]time**

**-b**

*real*

**-e**

*real*

**-ttol**

*real*

**-n**

*int*

**-[no]d**

**-bw**

*real*

**-[no]sham**

**-tsham**

*real*

**-pmin**

*real*

**-dim**

*vector*

**-ngrid**

*vector*

**-xmin**

*vector*

**-xmax**

*vector*

**-pmax**

*real*

**-gmax**

*real*

**-emin**

*real*

**-emax**

*real*

**-nlevels**

*int*

**-mname**

*string*

## DESCRIPTION

g_sham makes multi-dimensional free-energy, enthalpy and entropy plots. g_sham reads one or more xvg files and analyzes data sets. g_sham basic purpose is plotting 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 seperated 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 due to Kumar et. al. When also 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 r2 for a dimension 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.

## FILES

**-f**

*graph.xvg*

**Input**

**-ge*** gibbs.xvg*
**Input, Opt.**

**-ene*** esham.xvg*
**Input, Opt.**

**-dist*** ener.xvg*
**Output, Opt.**

**-histo*** edist.xvg*
**Output, Opt.**

**-bin*** bindex.ndx*
**Output, Opt.**

**-lp*** prob.xpm*
**Output, Opt.**

**-ls*** gibbs.xpm*
**Output, Opt.**

**-lsh*** enthalpy.xpm*
**Output, Opt.**

**-lss*** entropy.xpm*
**Output, Opt.**

**-map*** map.xpm*
**Output, Opt.**

**-ls3*** gibbs3.pdb*
**Output, Opt.**

**-mdata*** mapdata.xvg*
**Output, Opt.**

**-g*** shamlog.log*
**Output, Opt.**

## OTHER OPTIONS

**-[no]h**

*no*

**-nice*** int*** 19**

**-[no]w***no *

**-[no]xvgr***yes *

**-[no]time***yes *

**-b*** real*** -1 **

**-e*** real*** -1 **

**-ttol*** real*** 0 **

**-n*** int*** 1**

**-[no]d***no *

**-bw*** real*** 0.1 **

**-[no]sham***yes *

**-tsham*** real*** 298.15**

**-pmin*** real*** 0 **

**-dim*** vector*** 1 1 1**

**-ngrid*** vector*** 32 32 32**

**-xmin*** vector*** 0 0 0**

**-xmax*** vector*** 1 1 1**

**-pmax*** real*** 0 **

**-gmax*** real*** 0 **

**-emin*** real*** 0 **

**-emax*** real*** 0 **

**-nlevels*** int*** 25**

**-mname*** string*