.TH tpbconv 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
tpbconv - makes a run input file for restarting a crashed run

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3tpbconv\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.trr "
.BI "\-e" " ener.edr "
.BI "\-n" " index.ndx "
.BI "\-o" " tpxout.tpr "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-extend" " real "
.BI "\-until" " real "
.BI "\-nsteps" " int "
.BI "\-time" " real "
.BI "\-[no]zeroq" ""
.BI "\-[no]vel" ""
.BI "\-[no]cont" ""
.SH DESCRIPTION
\&tpbconv can edit run input files in four ways.


\&\fB 1.\fR by modifying the number of steps in a run input file
\&with options \fB \-extend\fR, \fB \-until\fR or \fB \-nsteps\fR
\&(nsteps=\-1 means unlimited number of steps)


\&\fB 2.\fR (OBSOLETE) by creating a run input file
\&for a continuation run when your simulation has crashed due to e.g.
\&a full disk, or by making a continuation run input file.
\&This option is obsolete, since mdrun now writes and reads
\&checkpoint files.
\&\fB Note\fR that a frame with coordinates and velocities is needed.
\&When pressure and/or Nose\-Hoover temperature coupling is used
\&an energy file can be supplied to get an exact continuation
\&of the original run.


\&\fB 3.\fR by creating a \fB .tpx\fR file for a subset of your original
\&tpx file, which is useful when you want to remove the solvent from
\&your \fB .tpx\fR file, or when you want to make e.g. a pure Calpha \fB .tpx\fR file.
\&Note that you may need to use \fB \-nsteps \-1\fR (or similar) to get
\&this to work.
\&\fB WARNING: this \fB .tpx\fR file is not fully functional\fR.


\&\fB 4.\fR by setting the charges of a specified group
\&to zero. This is useful when doing free energy estimates
\&using the LIE (Linear Interaction Energy) method.
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-f" " traj.trr" 
.B Input, Opt.
 Full precision trajectory: trr trj cpt 

.BI "\-e" " ener.edr" 
.B Input, Opt.
 Energy file 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " tpxout.tpr" 
.B Output
 Run input file: tpr tpb tpa 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 0" 
 Set the nicelevel

.BI "\-extend"  " real" " 0     " 
 Extend runtime by this amount (ps)

.BI "\-until"  " real" " 0     " 
 Extend runtime until this ending time (ps)

.BI "\-nsteps"  " int" " 0" 
 Change the number of steps

.BI "\-time"  " real" " \-1    " 
 Continue from frame at this time (ps) instead of the last frame

.BI "\-[no]zeroq"  "no    "
 Set the charges of a group (from the index) to zero

.BI "\-[no]vel"  "yes   "
 Require velocities from trajectory

.BI "\-[no]cont"  "yes   "
 For exact continuation, the constraints should not be applied before the first step

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.