gmx editconf [-f [<.gro/.g96/...>]] [-n [<.ndx>]] [-bf [<.dat>]] [-o [<.gro/.g96/...>]] [-mead [<.pqr>]] [-[no]w] [-[no]ndef] [-bt <enum>] [-box <vector>] [-angles <vector>] [-d <real>] [-[no]c] [-center <vector>] [-aligncenter <vector>] [-align <vector>] [-translate <vector>] [-rotate <vector>] [-[no]princ] [-scale <vector>] [-density <real>] [-[no]pbc] [-resnr <int>] [-[no]grasp] [-rvdw <real>] [-[no]sig56] [-[no]vdwread] [-[no]atom] [-[no]legend] [-label <string>] [-[no]conect]
The box can be modified with options
will center the system in the box, unless
-noc is used.
-center option can be used to shift the geometric center
of the system from the default of (x/2, y/2, z/2) implied by
to some other value.
-bt determines the box type:
triclinic is a
cubic is a rectangular box with all sides equal
dodecahedron represents a rhombic dodecahedron and
octahedron is a truncated octahedron.
The last two are special cases of a triclinic box.
The length of the three box vectors of the truncated octahedron is the
shortest distance between two opposite hexagons.
Relative to a cubic box with some periodic image distance, the volume of a
dodecahedron with this same periodic distance is 0.71 times that of the cube,
and that of a truncated octahedron is 0.77 times.
-box requires only
one value for a cubic, rhombic dodecahedral, or truncated octahedral box.
-d and a
triclinic box the size of the system in the x-,
and z-directions is used. With
octahedron boxes, the dimensions are set
to the diameter of the system (largest distance between atoms) plus twice
the specified distance.
-angles is only meaningful with option
a triclinic box and cannot be used with option
-ndef is set, a group
can be selected for calculating the size and the geometric center,
otherwise the whole system is used.
-rotate rotates the coordinates and velocities.
-princ aligns the principal axes of the system along the
coordinate axes, with the longest axis aligned with the x-axis.
This may allow you to decrease the box volume,
but beware that molecules can rotate significantly in a nanosecond.
Scaling is applied before any of the other operations are
performed. Boxes and coordinates can be scaled to give a certain density (option
-density). Note that this may be inaccurate in case a .gro
file is given as input. A special feature of the scaling option is that when the
factor -1 is given in one dimension, one obtains a mirror image,
mirrored in one of the planes. When one uses -1 in three dimensions,
a point-mirror image is obtained.
Groups are selected after all operations have been applied.
Periodicity can be removed in a crude manner. It is important that the box vectors at the bottom of your input file are correct when the periodicity is to be removed.
When writing .pdb files, B-factors can be
added with the
-bf option. B-factors are read
from a file with with following format: first line states number of
entries in the file, next lines state an index
followed by a B-factor. The B-factors will be attached per residue
unless the number of B-factors is larger than the number of the residues or unless the
-atom option is set. Obviously, any type of numeric data can
be added instead of B-factors.
-legend will produce
a row of CA atoms with B-factors ranging from the minimum to the
maximum value found, effectively making a legend for viewing.
With the option
-mead a special .pdb (.pqr)
file for the MEAD electrostatics
program (Poisson-Boltzmann solver) can be made. A further prerequisite
is that the input file is a run input file.
The B-factor field is then filled with the Van der Waals radius
of the atoms while the occupancy field will hold the charge.
-grasp is similar, but it puts the charges in the B-factor
and the radius in the occupancy.
-align allows alignment
of the principal axis of a specified group against the given vector,
with an optional center of rotation specified by
Finally, with option
editconf can add a chain identifier
to a .pdb file, which can be useful for analysis with e.g. Rasmol.
To convert a truncated octrahedron file produced by a package which uses a cubic box with the corners cut off (such as GROMOS), use:
gmx editconf -f in -rotate 0 45 35.264 -bt o -box veclen -o out
veclen is the size of the cubic box times sqrt(3)/2.
Options to specify input files:
-n[<.ndx>] (index.ndx) (Optional)
-bf[<.dat>] (bfact.dat) (Optional)
Generic data file
Options to specify output files:
-o[<.gro/.g96/…>] (out.gro) (Optional)
-mead[<.pqr>] (mead.pqr) (Optional)
Coordinate file for MEAD
Choose output from default index groups
Box type for
-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)
Distance between the solute and the box
Center molecule in box (implied by
-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)
-rotate<vector> (0 0 0)
Rotation around the X, Y and Z axes in degrees
Orient molecule(s) along their principal axes
-scale<vector> (1 1 1)
Density (g/L) of the output box achieved by scaling
Remove the periodicity (make molecule whole again)
Renumber residues starting from resnr
Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
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
Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
Read the Van der Waals radii from the file
vdwradii.datrather than computing the radii based on the force field
Force B-factor attachment per atom
Make B-factor legend
Add chain label for all residues
Add CONECT records to a .pdb file when written. Can only be done when a topology is present
For complex molecules, the periodicity removal routine may break down,
in that case you can use gmx trjconv.