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

6       gmx-solvate - Solvate a system
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SYNOPSIS

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

15       gmx solvate can do one of 2 things:
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17       1) Generate a box of solvent. Specify -cs and -box.  Or specify -cs and
18       -cp with a structure file with a box, but without atoms.
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20       2) Solvate a solute configuration, e.g. a protein, in a bath of solvent
21       molecules.  Specify  -cp (solute) and -cs (solvent).  The box specified
22       in the solute coordinate file (-cp) is used, unless -box  is  set.   If
23       you want the solute to be centered in the box, the program gmx editconf
24       has sophisticated options to change the box dimensions and  center  the
25       solute.   Solvent molecules are removed from the box where the distance
26       between any atom of the solute molecule(s) and any atom of the  solvent
27       molecule is less than the sum of the scaled van der Waals radii of both
28       atoms. A database (vdwradii.dat) of van der Waals radii is read by  the
29       program,  and  the  resulting  radii scaled by -scale. If radii are not
30       found in the database, those atoms are assigned the  (pre-scaled)  dis‐
31       tance  -radius.  Note that the usefulness of those radii depends on the
32       atom names, and thus varies widely with force field.
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34       The default solvent is Simple Point Charge water  (SPC),  with  coordi‐
35       nates  from  $GMXLIB/spc216.gro. These coordinates can also be used for
36       other 3-site water models, since a short  equibilibration  will  remove
37       the small differences between the models.  Other solvents are also sup‐
38       ported, as well as mixed solvents.  The  only  restriction  to  solvent
39       types  is  that a solvent molecule consists of exactly one residue. The
40       residue information in the coordinate files is used, and should  there‐
41       fore  be more or less consistent.  In practice this means that two sub‐
42       sequent solvent molecules in the solvent coordinate  file  should  have
43       different  residue  number.  The box of solute is built by stacking the
44       coordinates read from the coordinate file. This means that these  coor‐
45       dinates should be equlibrated in periodic boundary conditions to ensure
46       a good alignment of molecules on the stacking interfaces.  The  -maxsol
47       option  simply adds only the first -maxsol solvent molecules and leaves
48       out the rest that would have fitted into the box.  This  can  create  a
49       void that can cause problems later.  Choose your volume wisely.
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51       Setting  -shell  larger  than  zero  will place a layer of water of the
52       specified thickness (nm) around the solute. Hint: it is a good idea  to
53       put the protein in the center of a box first (using gmx editconf).
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55       Finally,  gmx  solvate  will optionally remove lines from your topology
56       file in which a number of solvent molecules is already added, and  adds
57       a  line  with  the total number of solvent molecules in your coordinate
58       file.
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OPTIONS

61       Options to specify input files:
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63       -cp [<.gro/.g96/…>] (protein.gro) (Optional)
64              Structure file: gro g96 pdb brk ent esp tpr
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66       -cs [<.gro/.g96/…>] (spc216.gro) (Library)
67              Structure file: gro g96 pdb brk ent esp tpr
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69       Options to specify input/output files:
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71       -p [<.top>] (topol.top) (Optional)
72              Topology file
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74       Options to specify output files:
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76       -o [<.gro/.g96/…>] (out.gro)
77              Structure file: gro g96 pdb brk ent esp
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79       Other options:
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81       -box <vector> (0 0 0)
82              Box size (in nm)
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84       -radius <real> (0.105)
85              Default van der Waals distance
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87       -scale <real> (0.57)
88              Scale factor to multiply Van der Waals radii from  the  database
89              in  share/gromacs/top/vdwradii.dat.  The  default  value of 0.57
90              yields density close to 1000 g/l for proteins in water.
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92       -shell <real> (0)
93              Thickness of optional water layer around solute
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95       -maxsol <int> (0)
96              Maximum number of solvent molecules to add if they  fit  in  the
97              box. If zero (default) this is ignored
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99       -[no]vel (no)
100              Keep velocities from input solute and solvent
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KNOWN ISSUES

103       · Molecules must be whole in the initial configurations.
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SEE ALSO

106       gmx(1)
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108       More     information    about    GROMACS    is    available    at    <‐
109       http://www.gromacs.org/>.
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112       2020, GROMACS development team
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1172019.6                           Feb 28, 2020                   GMX-SOLVATE(1)
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