gmx convert tpr
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gmx convert tpr [-s [<.tpr/.tpb/...>]] [-f [<.trr/.cpt/...>]] [-e [<.edr>]] [-n [<.ndx>]] [-o [<.tpr/.tpb/...>]] [-nice
] [-extend ] [-until ] [-nsteps ] [-time ] [-[no]zeroq] [-[no]vel] [-[no]cont] [-init_fep_state ]
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 This option is obsolete, since mdrun now writes and reads checkpoint files.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 Cα .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.