.\" Man page generated from reStructuredText. . .TH "GMX-CONVERT-TPR" "1" "Oct 28, 2016" "2016.1" "GROMACS" .SH NAME gmx-convert-tpr \- Make a modifed run-input file . .nr rst2man-indent-level 0 . .de1 rstReportMargin \\$1 \\n[an-margin] level \\n[rst2man-indent-level] level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] - \\n[rst2man-indent0] \\n[rst2man-indent1] \\n[rst2man-indent2] .. .de1 INDENT .\" .rstReportMargin pre: . RS \\$1 . nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] . nr rst2man-indent-level +1 .\" .rstReportMargin post: .. .de UNINDENT . RE .\" indent \\n[an-margin] .\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] .nr rst2man-indent-level -1 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] .in \\n[rst2man-indent\\n[rst2man-indent-level]]u .. .SH SYNOPSIS .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C gmx convert\-tpr [\fB\-s\fP \fI[<.tpr>]\fP] [\fB\-f\fP \fI[<.trr/.cpt/...>]\fP] [\fB\-e\fP \fI[<.edr>]\fP] [\fB\-n\fP \fI[<.ndx>]\fP] [\fB\-o\fP \fI[<.tpr>]\fP] [\fB\-extend\fP \fI\fP] [\fB\-until\fP \fI\fP] [\fB\-nsteps\fP \fI\fP] [\fB\-time\fP \fI\fP] [\fB\-[no]zeroq\fP] [\fB\-[no]vel\fP] [\fB\-[no]cont\fP] [\fB\-init_fep_state\fP \fI\fP] .ft P .fi .UNINDENT .UNINDENT .SH DESCRIPTION .sp \fBgmx convert\-tpr\fP can edit run input files in four ways. .sp \fB1.\fP by modifying the number of steps in a run input file with options \fB\-extend\fP, \fB\-until\fP or \fB\-nsteps\fP (nsteps=\-1 means unlimited number of steps) .sp \fB2.\fP (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 This option is obsolete, since mdrun now writes and reads checkpoint files. \fBNote\fP 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. .sp \fB3.\fP by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use \fB\-nsteps \-1\fP (or similar) to get this to work. \fBWARNING: this .tpx file is not fully functional\fP\&. .sp \fB4.\fP 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 OPTIONS .sp Options to specify input files: .INDENT 0.0 .TP .B \fB\-s\fP [<.tpr>] (topol.tpr) Portable xdr run input file .TP .B \fB\-f\fP [<.trr/.cpt/...>] (traj.trr) (Optional) Full precision trajectory: trr cpt tng .TP .B \fB\-e\fP [<.edr>] (ener.edr) (Optional) Energy file .TP .B \fB\-n\fP [<.ndx>] (index.ndx) (Optional) Index file .UNINDENT .sp Options to specify output files: .INDENT 0.0 .TP .B \fB\-o\fP [<.tpr>] (tprout.tpr) Portable xdr run input file .UNINDENT .sp Other options: .INDENT 0.0 .TP .B \fB\-extend\fP (0) Extend runtime by this amount (ps) .TP .B \fB\-until\fP (0) Extend runtime until this ending time (ps) .TP .B \fB\-nsteps\fP (0) Change the number of steps .TP .B \fB\-time\fP (\-1) Continue from frame at this time (ps) instead of the last frame .TP .B \fB\-[no]zeroq\fP (no) Set the charges of a group (from the index) to zero .TP .B \fB\-[no]vel\fP (yes) Require velocities from trajectory .TP .B \fB\-[no]cont\fP (yes) For exact continuation, the constraints should not be applied before the first step .TP .B \fB\-init_fep_state\fP (0) fep state to initialize from .UNINDENT .SH SEE ALSO .sp \fBgmx(1)\fP .sp More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>. .SH COPYRIGHT 2016, GROMACS development team .\" Generated by docutils manpage writer. .