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gmx-check - Online in the Cloud

Run gmx-check in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gmx-check that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-check - Check and compare files

SYNOPSIS


gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]] [-s1 [<.tpr>]]
[-s2 [<.tpr>]] [-c [<.tpr/.gro/...>]] [-e [<.edr>]]
[-e2 [<.edr>]] [-n [<.ndx>]] [-m [<.tex>]] [-vdwfac <real>]
[-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>]
[-abstol <real>] [-[no]ab] [-lastener <string>]

DESCRIPTION


gmx check reads a trajectory (.tng, .trr or .xtc), an energy file (.edr) or an index file
(.ndx) 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.

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, gmx check provides a quick check for such problems.

The program can compare two run input (.tpr) 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.

OPTIONS


Options to specify input files:

-f [<.xtc/.trr/...>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng

-f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng

-s1 [<.tpr>] (top1.tpr) (Optional)
Portable xdr run input file

-s2 [<.tpr>] (top2.tpr) (Optional)
Portable xdr run input file

-c [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent

-e [<.edr>] (ener.edr) (Optional)
Energy file

-e2 [<.edr>] (ener2.edr) (Optional)
Energy file

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-m [<.tex>] (doc.tex) (Optional)
LaTeX file

Other options:

-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]rmsd (no)
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]ab (no)
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.

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