*FILENAME: self-diffusion-coeff.inp
*PURPOSE: compute Mean Square Displacement vs time to get diffusion coeffcient D for water
* via the Einstein relation: 6*D is the slope of MSD vs t at long t.
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
*
!unix environment variable CHM_HOME points to CHARMM installation directory
read rtf card name $CHM_HOME/toppar/top_all22_prot.inp
read para card name $CHM_HOME/toppar/par_all22_prot.inp
read psf card name my_psf.psf

open unit 51 read unform name my_traj1.cor
open unit 52 read unform name my_traj2.cor

open unit 21 write form name msd.dat
write title unit 21
* TIME MSD
*

coor anal select type oh2 end - ! what atoms to look at, these are the TIP3 oxygens
firstu 51 nunit 2 skip 50 - ! trajectory specification
imsd 21 - ! flag to do the MSD analysis
rspin 0.0 rspout 999.9 - ! we are interested in ALL waters
ncors 200 - ! compute MSD out to NCORS*SKIP steps
xbox 40.0 ybox 45.0 zbox 45.0 ! and we did use PBC, simple rectangular box
! if trajectory is from constant pressure simulation
! actual box size is taken from trajectory
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden