1tpbconv(1)                GROMACS suite, VERSION 4.5                tpbconv(1)
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NAME

6       tpbconv - makes a run input file for restarting a crashed run
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8       VERSION 4.5
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SYNOPSIS

11       tpbconv -s topol.tpr -f traj.trr -e ener.edr -n index.ndx -o tpxout.tpr
12       -[no]h -[no]version -nice int -extend  real  -until  real  -nsteps  int
13       -time real -[no]zeroq -[no]vel -[no]cont
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DESCRIPTION

16       tpbconv can edit run input files in four ways.
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19        1st. by modifying the number of steps in a run input file with options
20       -extend,  -until or   -nsteps  (nsteps=-1  means  unlimited  number  of
21       steps)
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24         2nd.  (OBSOLETE)  by creating a run input file for a continuation run
25       when your simulation has crashed due to e.g.  a full disk, or by making
26       a  continuation  run  input file.  This option is obsolete, since mdrun
27       now writes and reads checkpoint files.  Note that a frame with  coordi‐
28       nates  and velocities is needed.  When pressure and/or Nose-Hoover tem‐
29       perature coupling is used an energy file can  be  supplied  to  get  an
30       exact continuation of the original run.
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33         3rd.  by  creating a tpx file for a subset of your original tpx file,
34       which is useful when you want to remove the solvent from your tpx file,
35       or  when  you want to make e.g. a pure Ca tpx file.   WARNING: this tpx
36       file is not fully functional.   4th. by setting the charges of a speci‐
37       fied  group  to  zero.  This is useful when doing free energy estimates
38       using the LIE (Linear Interaction Energy) method.
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FILES

41       -s topol.tpr Input
42        Run input file: tpr tpb tpa
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44       -f traj.trr Input, Opt.
45        Full precision trajectory: trr trj cpt
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47       -e ener.edr Input, Opt.
48        Energy file
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50       -n index.ndx Input, Opt.
51        Index file
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53       -o tpxout.tpr Output
54        Run input file: tpr tpb tpa
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OTHER OPTIONS

58       -[no]hno
59        Print help info and quit
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61       -[no]versionno
62        Print version info and quit
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64       -nice int 0
65        Set the nicelevel
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67       -extend real 0
68        Extend runtime by this amount (ps)
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70       -until real 0
71        Extend runtime until this ending time (ps)
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73       -nsteps int 0
74        Change the number of steps
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76       -time real -1
77        Continue from frame at this time (ps) instead of the last frame
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79       -[no]zeroqno
80        Set the charges of a group (from the index) to zero
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82       -[no]velyes
83        Require velocities from trajectory
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85       -[no]contyes
86        For exact continuation, the constraints should not be  applied  before
87       the first step
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SEE ALSO

91       gromacs(7)
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93       More   information  about  GROMACS  is  available  at  <http://www.gro‐
94       macs.org/>.
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98                                Thu 26 Aug 2010                     tpbconv(1)
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