*FILENAME: rmsd-rgyr.inp
*PURPOSE: compute rmsd vs initial structure and radius of gyration from trajectory
*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
read coor card name my_reference.crd
! put reference coordinates into comparison set as well
coor copy comp
open unit 11 write form name rmsd.dat
write title unit 11
* time rmsd
open unit 12 write form name rgyr.dat
write title unit 12
* time rgyr
! assume this is a trajectory where overall translation/rotation has been removed and
! without water or other unnecessary things
open unit 51 read unform name traj1.cor
open unit 52 read unform name traj2.cor
correl maxtime 10000
enter v1 rms
enter v2 gyra

traj firstu 51 nunit 2 begin 10500 skip 500 stop 55000

write v1 dumb time unit 11

write v2 dumb time unit 12


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden