Hi Kankana,
Your simulation box is too small.
The size of QM region + 2x QM cutoff in any x, y, and z direction must be smaller than two times the radius of largest sphere that fits inside the unit cell. This way the QM region plus cutoff on both sides will fit inside of the simulation box, even if the QM region rotates. In your case the radius is 11.536, which means that your box is only 2x 11.536 = 23.072 Angstrom in its smalles dimension. However, your QM region plus surrounding cutoff is as large as 27.501 Angstrom, which is larger and hence does not fit.
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On Jan 5, 2025, at 11:13 PM, Kankana Bhattacharjee via AMBER <amber.ambermd.org> wrote:
Dear AMBER users,
I am getting this error while running the QM-MM calculation. This is the
error:
ERROR: QM region + cutoff larger than box dimension:
QM-MM Cutoff = 8.0000
Coord Lower Upper Size Radius of largest sphere inside unit
cell
X -13.174 13.219 26.393 11.536
Y -14.552 12.950 27.501 11.536
Z -12.626 12.694 25.320 11.536
****************************************************
SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
QM region + cutoff larger than box
cannot continue, need larger box.
The box dimension is 10 angstrom. The cut-off is 8 angstrom.
I am attaching the qmmm.in file herewith. Kindly suggest. Shoudl I hav
eto make the bix dimension something like 12 or 15 angstrom ? Initially, I
tried with cutoff as 10 angstrom, but it dint work during equilibration
thats why hasd to make the cutoff as 8 angstrom and then it successfully
ran. Kindly suggest.
Thanks & Regards
Kankana Bhattacharjee
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Received on Mon Jan 06 2025 - 09:00:02 PST
