Thank you sir, Now that problem is fixed. I have reduced the QM region
cutoff to 6. and now getting the message like this:
--------------------------------------------------------------------------------
3.1 QM CALCULATION INFO
--------------------------------------------------------------------------------
Unable to correctly identify element O
Note: element guessing does not work with Hydrogen
Mass Repartitioning if ATOMIC_NUMBER is not
present in the topology file
How can I fix this ? Kindly suggest,.
Thanks & Regards
Kankana Bhattacharjee
On Mon, Jan 6, 2025 at 10:23 PM Goetz, Andreas <awgoetz.ucsd.edu> wrote:
> 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 - 09:30:02 PST
