Provided by: gromacs-data_2019.3-2_all bug


       gmx-solvate - Solvate a system


          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]


       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 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

       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 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 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>] ( (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


       · Molecules must be whole in the initial configurations.



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       2019, GROMACS development team