1 .TH tpbconv 1 "Fri 18 Jan 2013" "" "GROMACS suite, VERSION 4.5.6"
3 tpbconv - makes a run input file for restarting a crashed run
8 .BI "\-s" " topol.tpr "
10 .BI "\-e" " ener.edr "
11 .BI "\-n" " index.ndx "
12 .BI "\-o" " tpxout.tpr "
14 .BI "\-[no]version" ""
16 .BI "\-extend" " real "
17 .BI "\-until" " real "
18 .BI "\-nsteps" " int "
24 \&tpbconv can edit run input files in four ways.
27 \&\fB 1.\fR by modifying the number of steps in a run input file
28 \&with options \fB \-extend\fR, \fB \-until\fR or \fB \-nsteps\fR
29 \&(nsteps=\-1 means unlimited number of steps)
32 \&\fB 2.\fR (OBSOLETE) by creating a run input file
33 \&for a continuation run when your simulation has crashed due to e.g.
34 \&a full disk, or by making a continuation run input file.
35 \&This option is obsolete, since mdrun now writes and reads
37 \&\fB Note\fR that a frame with coordinates and velocities is needed.
38 \&When pressure and/or Nose\-Hoover temperature coupling is used
39 \&an energy file can be supplied to get an exact continuation
40 \&of the original run.
43 \&\fB 3.\fR by creating a \fB .tpx\fR file for a subset of your original
44 \&tpx file, which is useful when you want to remove the solvent from
45 \&your \fB .tpx\fR file, or when you want to make e.g. a pure Calpha \fB .tpx\fR file.
46 \&Note that you may need to use \fB \-nsteps \-1\fR (or similar) to get
48 \&\fB WARNING: this \fB .tpx\fR file is not fully functional\fR.
51 \&\fB 4.\fR by setting the charges of a specified group
52 \&to zero. This is useful when doing free energy estimates
53 \&using the LIE (Linear Interaction Energy) method.
55 .BI "\-s" " topol.tpr"
57 Run input file: tpr tpb tpa
61 Full precision trajectory: trr trj cpt
67 .BI "\-n" " index.ndx"
71 .BI "\-o" " tpxout.tpr"
73 Run input file: tpr tpb tpa
77 Print help info and quit
79 .BI "\-[no]version" "no "
80 Print version info and quit
82 .BI "\-nice" " int" " 0"
85 .BI "\-extend" " real" " 0 "
86 Extend runtime by this amount (ps)
88 .BI "\-until" " real" " 0 "
89 Extend runtime until this ending time (ps)
91 .BI "\-nsteps" " int" " 0"
92 Change the number of steps
94 .BI "\-time" " real" " \-1 "
95 Continue from frame at this time (ps) instead of the last frame
97 .BI "\-[no]zeroq" "no "
98 Set the charges of a group (from the index) to zero
100 .BI "\-[no]vel" "yes "
101 Require velocities from trajectory
103 .BI "\-[no]cont" "yes "
104 For exact continuation, the constraints should not be applied before the first step
109 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.