*FILENAME: dynamics.inp
*PURPOSE: very basic MD example of protein with xtal waters in vacuum
*AUTHOR: Lennart Nilsson, Karolinska Institutet, October 2003
*
! take psf and coordinates that were generated with gen-prot.inp and minimize.inp
! Unix environment variable CHM_HOME has to point to CHARMM installation directory

! Get definitions of amino acids and standard parameters
read rtf card name $CHM_HOME/toppar/top_all22_prot.inp
read param card name $CHM_HOME/toppar/par_all22_prot.inp

! Get psf and coordinates
read psf card name 4pti.psf
read coor card name 4pti_min.crd

open unit 12 write form name 4pti-dyn-0.res
open unit 21 write unform name 4pti-dyn-0.cor
open unit 22 write form name 4pti-dyn-0.mon
shake bonh param ! apply SHAKE on all bonds X-H
! heat from 48 K to 298 K in 10K increments every 500 steps
! then check temperature every 2000 steps to see that it is 298K +/-5K
! write out coordinates to trajectory every 100 steps
! save restart file at end
dynamics start time 0.002 nstep 10000 -
firstt 48.0 finalt 298.0 teminc 10.0 ihtfrq 500 -
ieqfrq 2000 ichecw 1 twindl -5.0 twindh +5.0 iasors 0 -
nprint 100 iprfrq 500 -
atom cdie fshift vshift cutnb 14.0 ctofnb 12.0 -
inbfrq -1 ihbfrq 0 - ! -1 for inbfrq/imgfrq means heuristic update
iunwrit 12 iuncrd 21 kunit 22 nsavc 100 !ie update nonbond list when any atom has move
! > 0.5 * (CUTNB-CTOFNB) since last update
write coor card name 4pti_dyn.crd
* 4pti coordinates after dynamics in vacuum, with xtal waters
*
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden