1GMX-DUMP(1) GROMACS GMX-DUMP(1)
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6 gmx-dump - Make binary files human readable
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9 gmx dump [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-e [<.edr>]]
10 [-cp [<.cpt>]] [-p [<.top>]] [-mtx [<.mtx>]] [-om [<.mdp>]]
11 [-[no]nr] [-[no]param] [-[no]sys] [-[no]orgir]
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14 gmx dump reads a run input file (.tpr), a trajectory (.trr/.xtc//tng),
15 an energy file (.edr) or a checkpoint file (.cpt) and prints that to
16 standard output in a readable format. This program is essential for
17 checking your run input file in case of problems.
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19 The program can also preprocess a topology to help finding problems.
20 Note that currently setting GMXLIB is the only way to customize direc‐
21 tories used for searching include files.
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24 Options to specify input files:
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26 -s [<.tpr>] (topol.tpr) (Optional)
27 Portable xdr run input file
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29 -f [<.xtc/.trr/…>] (traj.xtc) (Optional)
30 Trajectory: xtc trr cpt gro g96 pdb tng
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32 -e [<.edr>] (ener.edr) (Optional)
33 Energy file
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35 -cp [<.cpt>] (state.cpt) (Optional)
36 Checkpoint file
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38 -p [<.top>] (topol.top) (Optional)
39 Topology file
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41 -mtx [<.mtx>] (hessian.mtx) (Optional)
42 Hessian matrix
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44 Options to specify output files:
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46 -om [<.mdp>] (grompp.mdp) (Optional)
47 grompp input file with MD parameters
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49 Other options:
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51 -[no]nr (yes)
52 Show index numbers in output (leaving them out makes comparison
53 easier, but creates a useless topology)
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55 -[no]param (no)
56 Show parameters for each bonded interaction (for comparing
57 dumps, it is useful to combine this with -nonr)
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59 -[no]sys (no)
60 List the atoms and bonded interactions for the whole system
61 instead of for each molecule type
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63 -[no]orgir (no)
64 Show input parameters from tpr as they were written by the ver‐
65 sion that produced the file, instead of how the current version
66 reads them
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69 · Position restraint output from -sys -s is broken
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72 gmx(1)
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74 More information about GROMACS is available at <‐
75 http://www.gromacs.org/>.
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78 2020, GROMACS development team
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832019.6 Feb 28, 2020 GMX-DUMP(1)