Equilibration of solvated protein: equil.inp

Parameters to charmm:

*parameters*	*options*	*default*
pdbfile=	root of pdbfile name also segid of protein	none, die
toppar=	path to topology and parameter files	$toppar
crystal=	true, false	false
shape=	cubic, octahedral	cubic
begin=	number	1
end=	number	10
current=	number	@begin
status=	start, restart	start
task=	equil, format, unformat, unmerge	none, die

Required files and directories:

@toppar/top_all22_prot.inp
@toppar/par_all22_prot.inp
@pdbfile.psf
@pdbfile_solv-cube.crd or @pdbfile_solv-octa.crd
@pdbfile_dimens.stream
cubic.xtl or rhomba.xtl
kun/ output for energy prints
res/ directory of restart files
crd/ directory of output trajectories
coor/ output final coordinate files
size/ output files containing the box sizes

Equilibrate:

Do not run this job in workshop (very long) unless you change parameters of dynamics to shorten
the run. Output files are provided for analysis.

% charmm pdbfile=1fsc toppar="." crystal=true shape=octahedral \

         begin=1 end=10 task=equil < equil.inp > 1fsc_equil.out

gives output files:

% ls 1fsc_equil.out coor crd kun res size

1fsc_equil.out

coor:

1fsc_e1.chr    1fsc_e2.chr    1fsc_e4.chr    1fsc_e6.chr    1fsc_e8.chr

1fsc_e10.chr   1fsc_e3.chr    1fsc_e5.chr    1fsc_e7.chr    1fsc_e9.chr

crd:

1fsc_e1.crd    1fsc_e2.crd    1fsc_e4.crd    1fsc_e6.crd    1fsc_e8.crd

1fsc_e10.crd   1fsc_e3.crd    1fsc_e5.crd    1fsc_e7.crd    1fsc_e9.crd

kun:

1fsc_e1.kun    1fsc_e2.kun    1fsc_e4.kun    1fsc_e6.kun    1fsc_e8.kun

1fsc_e10.kun   1fsc_e3.kun    1fsc_e5.kun    1fsc_e7.kun    1fsc_e9.kun

res:

1fsc_e1.res    1fsc_e2.res    1fsc_e4.res    1fsc_e6.res    1fsc_e8.res

1fsc_e10.res   1fsc_e3.res    1fsc_e5.res    1fsc_e7.res    1fsc_e9.res

size:

1fsc_e1.size    1fsc_e2.size    1fsc_e4.size    1fsc_e6.size    1fsc_e8.size

1fsc_e10.size   1fsc_e3.size    1fsc_e5.size    1fsc_e7.size    1fsc_e9.size

These are all ascii files except the trajectory (crd) files and ascii files can be transferred between machines easily. The charmm trajectory files must often be formatted using DYNA FORMAT command to make transferrable files. Then DYNA UNFORMAT will remake native binary files on any machine that a hex formatted trajectory is copied to. For ease of tramsport, the "format" task of equil.inp first merges the trajectories together (as specified by begin= and end= parameters) before
formatting them. After transfer, a DYNA UNFORMAT will reproduce the binary merged trajectory.
The merged trajectory can then be split apart into the original files if desired with the "unmerge"task of equil.inp.

Example: moving the trajectory files from IBM SP3 to SGI R10000 Octane.