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GMX-SOLVATE(1)			     GROMACS			  GMX-SOLVATE(1)

NAME
     gmx-solvate - Solvate a system

SYNOPSIS
	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]

DESCRIPTION
     gmx solvate 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 gmx editconf has  sophis-
     ticated  options  to change the box dimensions and center the solute.  Sol-
     vent 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  (vd-
     wradii.dat)  of van der Waals radii is read by the program, and the result-
     ing radii scaled by -scale. If radii are not found in the	database,  those
     atoms  are  assigned the (pre-scaled) distance -radius.  Note that the use-
     fulness 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 condi-
     tions 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  speci-
     fied  thickness  (nm) around the solute. Hint: it is a good idea to put the
     protein in the center of a box first (using gmx editconf).

     Finally, gmx solvate 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.

OPTIONS
     Options to specify input files:

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

     -cs [<.gro/.g96/...>] (spc216.gro) (Library)
	    Structure file: gro g96 pdb 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: gro g96 pdb brk ent esp

     Other options:

     -box <vector> (0 0 0)
	    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

KNOWN ISSUES
     * Molecules must be whole in the initial configurations.

SEE ALSO
     gmx(1)

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

COPYRIGHT
     2026, GROMACS development team

2026.3				  Jun 25, 2026			  GMX-SOLVATE(1)
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