.. _gmx convert-tpr: gmx convert-tpr =============== Synopsis -------- .. parsed-literal:: gmx convert-tpr [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-f` :emphasis:`[<.trr/.cpt/...>]`] [:strong:`-e` :emphasis:`[<.edr>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.tpr>]`] [:strong:`-extend` :emphasis:``] [:strong:`-until` :emphasis:``] [:strong:`-nsteps` :emphasis:``] [:strong:`-time` :emphasis:``] [:strong:`-[no]zeroq`] [:strong:`-[no]vel`] [:strong:`-[no]cont`] [:strong:`-init_fep_state` :emphasis:``] Description ----------- ``gmx convert-tpr`` can edit run input files in four ways. **1.** by modifying the number of steps in a run input file with options ``-extend``, ``-until`` or ``-nsteps`` (nsteps=-1 means unlimited number of steps) **2.** (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 This option is obsolete, since mdrun now writes and reads checkpoint files. **Note** 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. **3.** 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 ``-nsteps -1`` (or similar) to get this to work. **WARNING: this .tpx file is not fully functional**. **4.** 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. Options ------- Options to specify input files: ``-s`` [<.tpr>] (topol.tpr) Portable xdr run input file ``-f`` [<.trr/.cpt/...>] (traj.trr) (Optional) Full precision trajectory: :ref:`trr` :ref:`cpt` :ref:`tng` ``-e`` [<.edr>] (ener.edr) (Optional) Energy file ``-n`` [<.ndx>] (index.ndx) (Optional) Index file Options to specify output files: ``-o`` [<.tpr>] (tprout.tpr) Portable xdr run input file Other options: ``-extend`` (0) Extend runtime by this amount (ps) ``-until`` (0) Extend runtime until this ending time (ps) ``-nsteps`` (0) Change the number of steps ``-time`` (-1) Continue from frame at this time (ps) instead of the last frame ``-[no]zeroq`` (no) Set the charges of a group (from the index) to zero ``-[no]vel`` (yes) Require velocities from trajectory ``-[no]cont`` (yes) For exact continuation, the constraints should not be applied before the first step ``-init_fep_state`` (0) fep state to initialize from .. only:: man See also -------- :manpage:`gmx(1)` More information about |Gromacs| is available at .