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