NAME

       gmx-sasa - Compute solvent accessible surface area

SYNOPSIS

          gmx sasa [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                   [-o [<.xvg>]] [-odg [<.xvg>]] [-or [<.xvg>]] [-oa [<.xvg>]]
                   [-tv [<.xvg>]] [-q [<.pdb>]] [-b <time>] [-e <time>]
                   [-dt <time>] [-tu <enum>] [-fgroup <selection>]
                   [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
                   [-selrpos <enum>] [-probe <real>] [-ndots <int>] [-[no]prot]
                   [-dgs <real>] [-surface <selection>] [-output <selection>]

DESCRIPTION

       gmx  sasa  computes solvent accessible surface areas.  See Eisenhaber F, Lijnzaad P, Argos P, Sander C, &
       Scharf M (1995) J. Comput. Chem. 16, 273-284 for the algorithm used.  With -q, the Connolly  surface  can
       be generated as well in a .pdb file where the nodes are represented as atoms and the edges connecting the
       nearest  nodes  as  CONECT  records.  -odg allows for estimation of solvation free energies from per-atom
       solvation energies per exposed surface area.

       The program requires a selection for the surface calculation to be specified with -surface.  This  should
       always  consist  of  all  non-solvent  atoms  in the system. The area of this group is always calculated.
       Optionally, -output can specify additional selections, which should be subsets of the calculation  group.
       The solvent-accessible areas for these groups are also extracted from the full surface.

       The average and standard deviation of the area over the trajectory can be calculated per residue and atom
       (options -or and -oa).

       With  the  -tv  option  the  total  volume  and  density  of the molecule can be computed. With -pbc (the
       default), you must ensure that your molecule/surface group is not split across PBC.  Otherwise, you  will
       get  non-sensical  results.   Please also 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.

OPTIONS

       Options to specify input files:

       -f [<.xtc/.trr/...>] (traj.xtc) (Optional)
              Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Input structure: tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Extra index groups

       Options to specify output files:

       -o [<.xvg>] (area.xvg)
              Total area as a function of time

       -odg [<.xvg>] (dgsolv.xvg) (Optional)
              Estimated solvation free energy as a function of time

       -or [<.xvg>] (resarea.xvg) (Optional)
              Average area per residue

       -oa [<.xvg>] (atomarea.xvg) (Optional)
              Average area per atom

       -tv [<.xvg>] (volume.xvg) (Optional)
              Total volume and density as a function of time

       -q [<.pdb>] (connolly.pdb) (Optional)
              PDB file for Connolly surface

       Other options:

       -b <time> (0)
              First frame (ps) to read from trajectory

       -e <time> (0)
              Last frame (ps) to read from trajectory

       -dt <time> (0)
              Only use frame if t MOD dt == first time (ps)

       -tu <enum> (ps)
              Unit for time values: fs, ps, ns, us, ms, s

       -fgroup <selection>
              Atoms stored in the trajectory file (if not set, assume first N atoms)

       -xvg <enum> (xmgrace)
              Plot formatting: xmgrace, xmgr, none

       -[no]rmpbc (yes)
              Make molecules whole for each frame

       -[no]pbc (yes)
              Use periodic boundary conditions for distance calculation

       -sf <file>
              Provide selections from files

       -selrpos <enum> (atom)
              Selection   reference   positions:   atom,  res_com,  res_cog,  mol_com,  mol_cog,  whole_res_com,
              whole_res_cog,   whole_mol_com,   whole_mol_cog,   part_res_com,    part_res_cog,    part_mol_com,
              part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog

       -probe <real> (0.14)
              Radius of the solvent probe (nm)

       -ndots <int> (24)
              Number of dots per sphere, more dots means more accuracy

       -[no]prot (yes)
              Output the protein to the Connolly .pdb file too

       -dgs <real> (0)
              Default value for solvation free energy per area (kJ/mol/nm^2)

       -surface <selection>
              Surface calculation selection

       -output <selection>
              Output selection(s)

SEE ALSO

       gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

COPYRIGHT

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                       GMX-SASA(1)