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tpbconv(1) [debian man page]

tpbconv(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					tpbconv(1)

NAME

       tpbconv - makes a run input file for restarting a crashed run

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       tpbconv	-s topol.tpr -f traj.trr -e ener.edr -n index.ndx -o tpxout.tpr -[no]h -[no]version -nice int -extend real -until real -nsteps int
       -time real -[no]zeroq -[no]vel -[no]cont

DESCRIPTION

       tpbconv 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  This option is obsolete, since mdrun now writes and reads checkpoint files.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  coor-
       dinates	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.

FILES

       -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

       -n index.ndx Input, Opt.
	Index file

       -o tpxout.tpr Output
	Run input file: tpr tpb tpa

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -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]zeroqno
	Set the charges of a group (from the index) to zero

       -[no]velyes
	Require velocities from trajectory

       -[no]contyes
	For exact continuation, the constraints should not be applied before the first step

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							tpbconv(1)

Check Out this Related Man Page

g_densorder(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				    g_densorder(1)

NAME

       g_densorder - calculate surface fluctuations

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_densorder -s topol.tpr -f traj.xtc -n index.ndx -o Density4D.dat -or hello.out -og interface.xpm -Spect intfspect.out -[no]h -[no]version
       -nice int -b time -e time -dt time -[no]w -[no]1d -bw real -bwn real -order int -axis string -method enum -d1 real  -d2	real  -tblock  int
       -nlevel int

DESCRIPTION

       A small program to reduce a two-phase density distribution along an axis, computed over a MD trajectory to 2D surfaces fluctuating in time,
       by a fit to a functional profile for interfacial densities A time-averaged spatial representation of the interfaces can be output with  the
       option -tavg

FILES

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -n index.ndx Input
	Index file

       -o Density4D.dat Output, Opt.
	Generic data file

       -or hello.out Output, Opt., Mult.
	Generic output file

       -og interface.xpm Output, Opt., Mult.
	X PixMap compatible matrix file

       -Spect intfspect.out Output, Opt., Mult.
	Generic output file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -b time 0
	First frame (ps) to read from trajectory

       -e time 0
	Last frame (ps) to read from trajectory

       -dt time 0
	Only use frame when t MOD dt = first time (ps)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -[no]1dno
	Pseudo-1d interface geometry

       -bw real 0.2
	Binwidth of density distribution tangential to interface

       -bwn real 0.05
	Binwidth of density distribution normal to interface

       -order int 0
	Order of Gaussian filter, order 0 equates to NO filtering

       -axis string Z
	Axis Direction - X, Y or Z

       -method enum bisect
	Interface location method:  bisect or  functional

       -d1 real 0
	Bulk density phase 1 (at small z)

       -d2 real 1000
	Bulk density phase 2 (at large z)

       -tblock int 100
	Number of frames in one time-block average

       -nlevel int 100
	Number of Height levels in 2D - XPixMaps

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						    g_densorder(1)
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