.TH g_sas 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_sas - computes solvent accessible surface area

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_sas\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-o" " area.xvg "
.BI "\-or" " resarea.xvg "
.BI "\-oa" " atomarea.xvg "
.BI "\-tv" " volume.xvg "
.BI "\-q" " connelly.pdb "
.BI "\-n" " index.ndx "
.BI "\-i" " surfat.itp "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-probe" " real "
.BI "\-ndots" " int "
.BI "\-qmax" " real "
.BI "\-[no]f_index" ""
.BI "\-minarea" " real "
.BI "\-[no]pbc" ""
.BI "\-[no]prot" ""
.BI "\-dgs" " real "
.SH DESCRIPTION
\&\fB g_sas\fR computes hydrophobic, hydrophilic and total solvent accessible surface area.
\&As a side effect, the Connolly surface can be generated as well in
\&a \fB .pdb\fR file where the nodes are represented as atoms and the vertices
\&connecting the nearest nodes as CONECT records.
\&The program will ask for a group for the surface calculation
\&and a group for the output. The calculation group should always
\&consists of all the non\-solvent atoms in the system.
\&The output group can be the whole or part of the calculation group.
\&The average and standard deviation of the area over the trajectory can be plotted
\&per residue and atom as well (options \fB \-or\fR and \fB \-oa\fR).
\&In combination with the latter option an \fB .itp\fR file can be
\&generated (option \fB \-i\fR)
\&which can be used to restrain surface atoms.


\&By default, periodic boundary conditions are taken into account,
\&this can be turned off using the \fB \-nopbc\fR option.


\&With the \fB \-tv\fR option the total volume and density of the molecule can be
\&computed.
\&Please consider whether the normal probe radius is appropriate
\&in this case or whether you would rather use e.g. 0. It is good
\&to keep in mind that the results for volume and density are very
\&approximate. For example, in ice Ih, one can easily fit water molecules in the
\&pores which would yield a volume that is too low, and surface area and density
\&that are both too high.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-o" " area.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-or" " resarea.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oa" " atomarea.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-tv" " volume.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-q" " connelly.pdb" 
.B Output, Opt.
 Protein data bank file 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-i" " surfat.itp" 
.B Output, Opt.
 Include file for topology 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version 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 \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-probe"  " real" " 0.14  " 
 Radius of the solvent probe (nm)

.BI "\-ndots"  " int" " 24" 
 Number of dots per sphere, more dots means more accuracy

.BI "\-qmax"  " real" " 0.2   " 
 The maximum charge (e, absolute value) of a hydrophobic atom

.BI "\-[no]f_index"  "no    "
 Determine from a group in the index file what are the hydrophobic atoms rather than from the charge

.BI "\-minarea"  " real" " 0.5   " 
 The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file  (see help)

.BI "\-[no]pbc"  "yes   "
 Take periodicity into account

.BI "\-[no]prot"  "yes   "
 Output the protein to the Connelly \fB .pdb\fR file too

.BI "\-dgs"  " real" " 0     " 
 Default value for solvation free energy per area (kJ/mol/nm2)

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.