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.
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
