*  =========================================
*  JOB: evalrmsd: rmsd of atom positions
*

bomb -2

! { parameters passed }
set dcd wt.10ns
set inp wt_lz.dyna_desolv

open unit 1 card read name ../lib/top_all27_prot_na.rtf
read RTF card unit 1
close unit 1

open unit 1 card read name ../lib/par_all27_prot_na.prm
read PARA card unit 1
close unit 1

stream ../lib/aco.rtf

open unit 1 read formatted name ../scr/@inp.psf
read psf card unit 1
close unit 1
open read formatted unit 17 name ../scr/@inp.crd
read coor card unit 17
coor copy comp

! atom definitions
define nonh sele ( .not. hydrogen ) end
define back sele ( type n .or. type ca .or. type c ) end
define main sele ( type n .or. type ca .or. type c .or. type o .or. type ot1 -
                   .or. type ot2 ) end
define side sele ( ( .not. main ) ) end

COORdinate COPY COMParison

define RMSD sele ( segid L .AND. back ) end
define reorientation sele ( segid L .AND. back ) end 
set reor reorientation  ! selection for reorientation
set rms RMSD ! calculate the RMS for this selection

! trajectory
open unit 13 read unfor name ../scr/@dcd.cor

! result file
open unit 2 write formatted name ../scr/prod1.evalrmsd.rms

! make the RMSD timeseries, save to file
CORREL MAXSERIES 1 MAXTIMESTEPS 10000000 MAXATOMS 50000
ENTER RMSD RMS
TRAJECTORY FIRSTU  13 NUNIT 1 -
   SELECT @rms END -
   ORIENT SELECT @reor END
WRITE RMSD UNIT 2 DUMB TIME

END

STOP