This is the command gmx-convert-tpr that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-convert-tpr - Make a modifed run-input file
SYNOPSIS
gmx convert-tpr [-s [<.tpr>]] [-f [<.trr/.cpt/...>]] [-e [<.edr>]]
[-n [<.ndx>]] [-o [<.tpr>]] [-extend <real>]
[-until <real>] [-nsteps <int>] [-time <real>]
[-[no]zeroq] [-[no]vel] [-[no]cont]
[-init_fep_state <int>]
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is obsolete, since mdrun now writes and reads checkpoint files.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: trr cpt 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 <real> (0)
Extend runtime by this amount (ps)
-until <real> (0)
Extend runtime until this ending time (ps)
-nsteps <int> (0)
Change the number of steps
-time <real> (-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 <int> (0)
fep state to initialize from
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