gmx-solvate - Solvate a system

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                    GMX-SOLVATE(1)

gmxsolvate can do one of 2 things:

       1)  Generate a box of solvent. Specify -cs and -box.  Or specify -cs and -cp with a structure file with a
       box, but without atoms.

       2) Solvate a solute configuration, e.g. a protein, in a bath of solvent molecules. Specify  -cp  (solute)
       and  -cs  (solvent).   The box specified in the solute coordinate file (-cp) is used, unless -box is set.
       If you want the solute to be centered in the box, the program gmxeditconf has sophisticated  options  to
       change  the  box  dimensions and center the solute.  Solvent molecules are removed from the box where the
       distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the
       sum of the scaled van der Waals radii of both atoms. A database (vdwradii.dat) of van der Waals radii  is
       read  by  the  program, and the resulting radii scaled by -scale. If radii are not found in the database,
       those atoms are assigned the (pre-scaled) distance -radius.  Note that  the  usefulness  of  those  radii
       depends on the atom names, and thus varies widely with force field.

       The  default  solvent is Simple Point Charge water (SPC), with coordinates from $GMXLIB/spc216.gro. These
       coordinates can also be used for other 3-site water models, since a short equibilibration will remove the
       small differences between the models.  Other solvents are also supported, as well as mixed solvents.  The
       only restriction to solvent types is that a solvent molecule consists of exactly one residue. The residue
       information  in  the  coordinate  files  is  used,  and  should therefore be more or less consistent.  In
       practice this means that two subsequent solvent molecules in the  solvent  coordinate  file  should  have
       different  residue  number.   The  box  of  solute  is  built  by  stacking the coordinates read from the
       coordinate file. This means that these coordinates should be equlibrated in periodic boundary  conditions
       to  ensure a good alignment of molecules on the stacking interfaces.  The -maxsol option simply adds only
       the first -maxsol solvent molecules and leaves out the rest that would have fitted into the box. This can
       create a void that can cause problems later.  Choose your volume wisely.

       Setting -shell larger than zero will place a layer of water of the specified thickness  (nm)  around  the
       solute. Hint: it is a good idea to put the protein in the center of a box first (using gmxeditconf).

       Finally,  gmxsolvate  will optionally remove lines from your topology file in which a number of solvent
       molecules is already added, and adds a line with the total number of solvent molecules in your coordinate
       file.

       • Molecules must be whole in the initial configurations.

       gmx-solvate - Solvate a system

       Options to specify input files:

       -cp[<.gro/.g96/...>](protein.gro)(Optional)
              Structure file: grog96pdb brk ent esp tpr-cs[<.gro/.g96/...>](spc216.gro)(Library)
              Structure file: grog96pdb brk ent esp tpr

       Options to specify input/output files:

       -p[<.top>](topol.top)(Optional)
              Topology file

       Options to specify output files:

       -o[<.gro/.g96/...>](out.gro)
              Structure file: grog96pdb brk ent esp

       Other options:

       -box<vector>(000)
              Box size (in nm)

       -radius<real>(0.105)
              Default van der Waals distance

       -scale<real>(0.57)
              Scale factor to multiply Van der Waals radii from the database in  share/gromacs/top/vdwradii.dat.
              The default value of 0.57 yields density close to 1000 g/l for proteins in water.

       -shell<real>(0)
              Thickness of optional water layer around solute

       -maxsol<int>(0)
              Maximum  number  of  solvent  molecules  to  add if they fit in the box. If zero (default) this is
              ignored

       -[no]vel(no)
              Keep velocities from input solute and solvent

gmx(1)

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

          gmx solvate [-cp[<.gro/.g96/...>]] [-cs[<.gro/.g96/...>]]
                      [-p[<.top>]] [-o[<.gro/.g96/...>]] [-box<vector>]
                      [-radius<real>] [-scale<real>] [-shell<real>]
                      [-maxsol<int>] [-[no]vel]