Talk:Mod:Hunt Research Group/Visualising

After setup, NPT equilibration and running your NVT(NVE) simulation you will want to analyse your production phase trajectory.

1. Confirm your production run is actually equilibrated (same as what you did for the equilibration phase using CCP1GUI).

2. To visualise the atoms moving use VMD

http://www.ks.uiuc.edu/Research/vmd/

(follow their setup instructions)

transfer the HISTORY file to your local computer

FILE:NEW MOLECULE

BROWSE and choose the HISTORY file

select DLPOLY V2 as the file format

LOAD

if your file loads with bonds stretching across the screen

select GRAPHICS

under Drawing Method choose DYNAMIC BONDS

modify the bond cut-off so that bonded molecules are bonded

then reduce the bond radius to more stick like structure

check that your box has not exploded, a few molecules outside is ok, but not an increasing number of molecules, also it should be cube like and not deformed if the box does deform you may have a box dimension too large/small and you should go back and complete a npt equilibration.

time guesstimates

for 4000 atoms,1ns=1000ps per day on 8proc