*FILENAME: trp-anisotropy.inp
*PURPOSE: compute Trp fluorescence anisotropy decay
*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

! assume this is a trajectory where overall translation/rotation has been removed
! see merge-orient-trajectory.inp
open unit 51 read unform name traj1.cor
open unit 52 read unform name traj2.cor

correl maxtime 10000 noupdate ! we don't need any list update, and have no coordinates
! we will compute the anisotropy of the La and Lb transition dipoles, see correl.doc

enter la vector xyz prot 7 NE1 prot 7 CZ3 prot 7 NE1 prot 7 CE3
enter lb vector xyz prot 7 CD1 prot 7 CH2 prot 7 CD1 prot 7 CZ3

traj firstu 51 nunit 2 begin 10500 skip 500 ! read the trajectory to the end

mantime la normal
! the default for the P2 correlation is to use the FFT
! you may want to compare this result with "corfun la la P2 direct"
! if they differ you should look at
! www.charmm.org -> forums -> Bug report&fixes -> PGI problem with corfun
corfun la la p2
open unit 31 write form name trp-aniso-la.dat
write title unit 31
* time r(t)
*
write corr dumb time unit 31
*hi
*
close unit 31
mantime lb normal
corfun lb lb p2
open unit 31 write form name trp-aniso-lb.dat
write title unit 31
* time r(t)
*
write corr dumb time unit 31
*hi
*

end
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden