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gmxcheckMain Table of Contents |
VERSION 3.1
Thu 28 Feb 2002
| VERSION 3.1 |
gmxcheck reads a trajectory (.trj, .trr or .xtc) or an energy file (.ene or .edr) and prints out useful information 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.
The program will compare run input (.tpr, .tpb or .tpa) files when both -s1 and -s2 are supplied.
| option | filename | type | description |
|---|---|---|---|
| -f | traj.xtc | Input, Opt. | Generic trajectory: xtc trr trj gro g96 pdb |
| -f2 | traj.xtc | Input, Opt. | Generic trajectory: xtc trr trj gro g96 pdb |
| -s1 | top1.tpr | Input, Opt. | Generic run input: tpr tpb tpa |
| -s2 | top2.tpr | Input, Opt. | Generic run input: tpr tpb tpa |
| -c | topol.tpr | Input, Opt. | Structure+mass(db): tpr tpb tpa gro g96 pdb |
| -e | ener.edr | Input, Opt. | Generic energy: edr ene |
| -e2 | ener2.edr | Input, Opt. | Generic energy: edr ene |
| option | type | default | description |
|---|---|---|---|
| -[no]h | bool | no | Print help info and quit |
| -[no]X | bool | no | Use dialog box GUI to edit command line options |
| -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 |
| -tol | real | 0 | Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) |
| -lastener | string | Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. |