g_nmtraj(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_nmtraj(1)NAME
g_nmtraj - generate a virtual trajectory from an eigenvector
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_nmtraj -s topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -[no]version -nice int -eignr string -phases string -temp real -amplitude real
-nframes int
DESCRIPTION
g_nmtraj generates an virtual trajectory from an eigenvector, corresponding to a harmonic Cartesian oscillation around the average struc-
ture. The eigenvectors should normally be mass-weighted, but you can use non-weighted eigenvectors to generate orthogonal motions. The
output frames are written as a trajectory file covering an entire period, and the first frame is the average structure. If you write the
trajectory in (or convert to) PDB format you can view it directly in PyMol and also render a photorealistic movie. Motion amplitudes are
calculated from the eigenvalues and a preset temperature, assuming equipartition of the energy over all modes. To make the motion clearly
visible in PyMol you might want to amplify it by setting an unrealistically high temperature. However, be aware that both the linear
Cartesian displacements and mass weighting will lead to serious structure deformation for high amplitudes - this is is simply a limitation
of the Cartesian normal mode model. By default the selected eigenvector is set to 7, since the first six normal modes are the transla-
tional and rotational degrees of freedom.
FILES -s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-v eigenvec.trr Input
Full precision trajectory: trr trj cpt
-o nmtraj.xtc Output
Trajectory: xtc trr trj gro g96 pdb
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-eignr string 7
String of eigenvectors to use (first is 1)
-phases string 0.0
String of phases (default is 0.0)
-temp real 300
Temperature in Kelvin
-amplitude real 0.25
Amplitude for modes with eigenvalue=0
-nframes int 30
Number of frames to generate
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_nmtraj(1)
Check Out this Related Man Page
gmxcheck(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c gmxcheck(1)NAME
gmxcheck - checks and compares files
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
gmxcheck -f traj.xtc -f2 traj.xtc -s1 top1.tpr -s2 top2.tpr -c topol.tpr -e ener.edr -e2 ener2.edr -n index.ndx -m doc.tex -[no]h -[no]ver-
sion -nice int -vdwfac real -bonlo real -bonhi real -[no]rmsd -tol real -abstol real -[no]ab -lastener string
DESCRIPTION
gmxcheck reads a trajectory ( .trj, .trr or .xtc), an energy file ( .ene or .edr) or an index file ( .ndx) and prints out useful infor-
mation about them.
Option -c checks for presence of coordinates, velocities and box in the file, for close contacts (smaller than -vdwfac and not bonded,
i.e. not between -bonlo and -bonhi, all relative to the sum of both Van der Waals radii) and atoms outside the box (these may occur often
and are no problem). If velocities are present, an estimated temperature will be calculated from them.
If an index file, is given its contents will be summarized.
If both a trajectory and a .tpr file are given (with -s1) the program will check whether the bond lengths defined in the tpr file are
indeed correct in the trajectory. If not you may have non-matching files due to e.g. deshuffling or due to problems with virtual sites.
With these flags, gmxcheck provides a quick check for such problems.
The program can compare two run input ( .tpr, .tpb or .tpa) files when both -s1 and -s2 are supplied. Similarly a pair of trajectory
files can be compared (using the -f2 option), or a pair of energy files (using the -e2 option).
For free energy simulations the A and B state topology from one run input file can be compared with options -s1 and -ab.
In case the -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper.
FILES -f traj.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-f2 traj.xtc Input, Opt.
Trajectory: xtc trr trj gro g96 pdb cpt
-s1 top1.tpr Input, Opt.
Run input file: tpr tpb tpa
-s2 top2.tpr Input, Opt.
Run input file: tpr tpb tpa
-c topol.tpr Input, Opt.
Structure+mass(db): tpr tpb tpa gro g96 pdb
-e ener.edr Input, Opt.
Energy file
-e2 ener2.edr Input, Opt.
Energy file
-n index.ndx Input, Opt.
Index file
-m doc.tex Output, Opt.
LaTeX file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 0
Set the nicelevel
-vdwfac real 0.8
Fraction of sum of VdW radii used as warning cutoff
-bonlo real 0.4
Min. fract. of sum of VdW radii for bonded atoms
-bonhi real 0.7
Max. fract. of sum of VdW radii for bonded atoms
-[no]rmsdno
Print RMSD for x, v and f
-tol real 0.001
Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)
-abstol real 0.001
Absolute tolerance, useful when sums are close to zero.
-[no]abno
Compare the A and B topology from one file
-lastener string
Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 gmxcheck(1)