On Wed, Apr 27, 2022, Pau Mayorga Delgado wrote:
>
>I am performing a QM simulation for two hexanol molecules (dimer) in water. The problem is that the MD keeps stopping with the same error:
>
> ****************************************************
> ERROR: QM region + cutoff larger than box dimension:
> QM-MM Cutoff = 9.0000
> Coord Lower Upper Size Radius of largest sphere inside unit cell
> X -13.798 14.995 28.793 19.837
> Y -14.031 15.206 29.237 19.837
> Z -18.739 20.939 39.679 19.837
> ****************************************************
> SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
> QM region + cutoff larger than box
> cannot continue, need larger box.
>
>I suspect that the reason is because the two molecules don't stay
>together. A possible solution would be to increase the QM region, but I
>don't think that would work, because if the molecules separate, given long
>enough MD trajectories we would always run out of space in the QM box. The
>question is: is there a way to put restrains on those molecules so that
>they stay within the QM region for the whole trajectory?
The QM region is defined by the atoms it contains, but the region needs to
be "compact". Ambe is not set up to having the quantum region consist of
two molecules that are far apart from each other.
There are various ways to artificially tether two molecules together: these
are generally called "NMR restraints" in the documentation, since terms like
this were first widely used for NMR refinements.
...hope this helps....dac
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Received on Fri Apr 29 2022 - 19:00:02 PDT
