Mod:Hunt Research Group/dl poly basics

DL_POLY basics

files

• CONTROL file -specifies program run controls
• CONFIG file -specifies starting conditions, ie geometry
• FIELD file -specifies the forcefield
• OUTPUT file -summary output
• REVIVE file -not human readable contains restart information
• REVCON file -contains the final configuration
• STATIS file -contains step-wise record of thermodynamic variables
• HISTORY file -contains trajectory

viewing

• use VMD to view the config files
• in general: open VMD choose extensions and TK console, in the console type logfile console

then type "source script.tcl" to load a script

then type "script.tcl" to run the script

• here is a script that automatically loads the file with good viewing options switched on

save this as load_vmd.tcl

load the script by typing source load_vmd.tcl

run the script by typing load

to view the REVCON replace CONFIG, save the file, reload it and then execute again

proc load {args} {
#setup some display settings first
# set the background colour
# all atoms same size=orthographic depth=perspective
# turn off the depth shading
# turn off the axes
color Display Background iceblue
display projection   Orthographic
display nearclip set 0.000000
display farclip  set 10.000000
display depthcue   off
axes location off
#
# read in new molecule
mol new CONFIG type dlpolyconfig

# deleate top rep (lines)
mol delrep 0 top
# add cpk rep to everything
# sphere_scale=1.2 sphere_res=20 bond_radius=0.5 bond_resolution=16
mol selection {all}
mol representation CPK 1.100000 0.300000 20.000000 16.000000
# colour atoms by their name
mol color Name
# now add to the graphics window
mol addrep top

}