GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages


Manual Reference Pages  -  GMX-CHECK (1)

NAME

gmx-check - Check and compare files

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

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

DESCRIPTION

gmx check reads a trajectory (.trj, .trr or .xtc), an energy file (.ene or .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, .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.

OPTIONS

Options to specify input and output files:

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

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

-s1 [<.tpr/.tpb/...>] (top1.tpr) (Input, Optional)
Run input file: tpr tpb tpa

-s2 [<.tpr/.tpb/...>] (top2.tpr) (Input, Optional)
Run input file: tpr tpb tpa

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

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

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

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

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

Other 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

-[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.

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

Search for    or go to Top of page |  Section 1 |  Main Index


VERSION 5.0.6 GMX-CHECK (1)

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.