分析梳理--分子动力学模拟的常规步骤二（Gromacs）

Options to specify input files:

 -f      [<.gro/.g96/...>]  (conf.gro)
           Structure file: gro g96 pdb brk ent esp tpr
 -n      [<.ndx>]           (index.ndx)      (Opt.)
           Index file
 -bf     [<.dat>]           (bfact.dat)      (Opt.)
           Generic data file

Options to specify output files:

 -o      [<.gro/.g96/...>]  (out.gro)        (Opt.)
           Structure file: gro g96 pdb brk ent esp
 -mead   [<.pqr>]           (mead.pqr)       (Opt.)
           Coordinate file for MEAD

Other options:

 -[no]w                     (no)
           View output .xvg, .xpm, .eps and .pdb files
 -[no]ndef                  (no)
           Choose output from default index groups
 -bt     <enum>             (triclinic)
           Box type for -box and -d: triclinic, cubic, dodecahedron,
           octahedron
 -box    <vector>           (0 0 0)
           Box vector lengths (a,b,c)
 -angles <vector>           (90 90 90)
           Angles between the box vectors (bc,ac,ab)
 -d      <real>             (0)
           Distance between the solute and the box
 -[no]c                     (no)
           Center molecule in box (implied by -box and -d)
 -center <vector>           (0 0 0)
           Shift the geometrical center to (x,y,z)
 -aligncenter <vector>      (0 0 0)
           Center of rotation for alignment
 -align  <vector>           (0 0 0)
           Align to target vector
 -translate <vector>        (0 0 0)
           Translation
 -rotate <vector>           (0 0 0)
           Rotation around the X, Y and Z axes in degrees
 -[no]princ                 (no)
           Orient molecule(s) along their principal axes
 -scale  <vector>           (1 1 1)
           Scaling factor
 -density <real>            (1000)
           Density (g/L) of the output box achieved by scaling
 -[no]pbc                   (no)
           Remove the periodicity (make molecule whole again)
 -resnr  <int>              (-1)
            Renumber residues starting from resnr
 -[no]grasp                 (no)
           Store the charge of the atom in the B-factor field and the radius
           of the atom in the occupancy field
 -rvdw   <real>             (0.12)
           Default Van der Waals radius (in nm) if one can not be found in the
           database or if no parameters are present in the topology file
 -[no]sig56                 (no)
           Use rmin/2 (minimum in the Van der Waals potential) rather than
           sigma/2
 -[no]vdwread               (no)
           Read the Van der Waals radii from the file vdwradii.dat rather than
           computing the radii based on the force field
 -[no]atom                  (no)
           Force B-factor attachment per atom
 -[no]legend                (no)
           Make B-factor legend
 -label  <string>           (A)
           Add chain label for all residues
 -[no]conect                (no)
           Add CONECT records to a .pdb file when written. Can only be done
           when a topology (tpr file) is present

KNOWN ISSUES

* For complex molecules, the periodicity removal routine may break down,
* in that case you can use gmx trjconv.

gmx editconf -f conf.gro -o newbox.gro -c -bt cubic -d 1.0

Options to specify input files:

 -cp     [<.gro/.g96/...>]  (protein.gro)    (Opt.)
           Structure file: gro g96 pdb brk ent esp tpr
 -cs     [<.gro/.g96/...>]  (spc216.gro)     (Lib.)
           Structure file: gro g96 pdb brk ent esp tpr

Options to specify input/output files:

 -p      [<.top>]           (topol.top)      (Opt.)
           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

gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro