tpbconv

VERSION 4.0_rc1
Mon 22 Sep 2008

Description

tpbconv can edit run input files in four ways.

1st. by modifying the number of steps in a run input file with option -nsteps or option -runtime.

2st. (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 This option is obsolete, since mdrun now writes and reads checkpoint files.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.

3nd. 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 Ca tpx file. WARNING: this tpx file is not fully functional. 4rd. 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.

Files

option	filename	type	description
`-s`	`topol.tpr`	Input	Run input file: tpr tpb tpa
`-f`	`traj.trr`	Input, Opt.	Full precision trajectory: trr trj cpt
`-e`	`ener.edr`	Input, Opt.	Energy file: edr ene
`-n`	`index.ndx`	Input, Opt.	Index file
`-o`	`tpxout.tpr`	Output	Run input file: tpr tpb tpa

Other options

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-nice`	int	`0`	Set the nicelevel
`-nsteps`	int	`-1`	Change the number of steps
`-runtime`	real	`-1`	Set the run time (ps)
`-time`	real	`-1`	Continue from frame at this time (ps) instead of the last frame
`-extend`	real	`0`	Extend runtime by this amount (ps)
`-until`	real	`0`	Extend runtime until this ending time (ps)
`-[no]zeroq`	bool	`no`	Set the charges of a group (from the index) to zero
`-[no]cont`	bool	`yes`	For exact continuation, the constraints should not be solved before the first step

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