Thanks a lot for the rectification.
One thing I am curious about:
When running a simulation for a long time it might grow or shrink over time so the crystal data (side length of box in particular) I used to setup the simulation is "outdated".
When using "correl" or "update" with crystal information I ran into the following error:
***** LEVEL -1 WARNING FROM <TSTCRD> *****
***** SOME ATOM COORDINATES UNDEFINED OR OUT OF RANGE
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5
Here's the example code:
! Read in Topology and Parameter files
stream ../read_psf_and_toppar.str
! Setup Crystal
crystal define TETR 93.7831 93.7831 144.964 90 90 90
open unit 1 read card name crystal.xtl
crystal read unit 1 card
close unit 1
! Image centering
image byresid XCEN 0.0 YCEN 0.0 ZCEN 0.0 sele ALL .and. .not. segid PRO* .and. .not. segid RNAA end
image byseg XCEN 0.0 YCEN 0.0 ZCEN 0.0 sele segid RNAA .or. segid PRO* end
open unit 99 file read name concatenated_recentered.dcd
traj query unit 99
calc NSTEP ?nstep
set START ?start
calc STOP ?nstep
set SKIP ?skip
calc mxa 9164 + 40334
calc mxs 6
calc mxt @NSTEP
correl maxtim @MXT maxa @MXA maxs @MXS
define MS sele segid MEMB end
define PS sele segid PRO* end
end
stop
The crystal.xtl was written with the "write crystal" command after solvating, neutralizing, centering and shaping the system.
When I omit the "read crystal.xtl" line, the error is gone.
Adding the "noupdate" option to "correl" omits the error as expected.
Or does this not at all relate to the side length of the box?
Cheers,
Bjoern
