Re: [AMBER] Reg:QM region + cutoff larger than box dimension

From: Ross Walker <>
Date: Thu, 6 Oct 2011 09:50:52 -0700

Hi Kaustubh

Have you checked that you can successfully run classical MD with this system
before switching to QMMM? Your box looks very ordered with many gaps between
molecules suggesting it is a long way from being equilibrated. You should
probably heat and equilibrate the density classically before swithing on the
QM/MM. Also taking a look at the final frame of your 4A trajectory shows
that the system crashed because you actually made hydrogen and this molecule
took off.

Your box is also VERY small. You have 28 x 23 x 27 angstroms at the initial
structure. Looking at your QM region it spans approximately 10 angstroms. So
with an 8 angstrom QM cut off your QM region consist of a MM shell that is 8
+ 10 + 8 angstroms across at the thickest point. This gives you 26
angstroms. Hence the second your box shrinks in size because it equilibrated
and the density increased or your QM region rotates such that the longest
axis points along the shortest (23 angstrom) dimension of your box so you
violate the minimum image convention and the calculation stops.

The 4 angstrom qmcut run worked because this would be 18 angstroms which
fits in your small box. However, the 4 angstrom cut is giving you wild QM/MM
interactions and as you can see from your trajectory you get a pair of
hydrogens ejected which form H2 and move away from the central QM region.
This expands your QM region size and as soon as QMcut+ QMsize + Qmcut is
greater than your box dimension so the calculation stops.

The simple solution is to make your box much bigger. I would suggest at
least 35 ansgtroms in each direction. You might need more if you expect the
molecules in your QM region to dissociate in some way.

I would also carefully equilibrate the system classical and then further
equilibrate with QMMM before attempting to do the umbrella sampling.

Good luck,

> -----Original Message-----
> From: kaustubh joshi []
> Sent: Thursday, October 06, 2011 7:46 AM
> To:
> Subject: [AMBER] Reg:QM region + cutoff larger than box dimension
> HI ALL!!
> I have generated a one molar system with 4 solute
> molecules. I have to carry out and umbrella sampling for this system
> wherein
> a proton is transferred from phenol to the imine. Out of all the
> phenol-imine residues present in the system,I am considering residues
> 22 and
> 23 for the proton transfer. My problem is the calculations stop with
> error:
> ERROR: QM region + cutoff larger than box dimension:
> QM-MM Cutoff = 4.0000
> Coord Lower Upper Size Radius of largest sphere inside
> unit
> cell
> X -9.745 9.611 19.357 11.528
> Y -5.919 11.077 16.996 11.528
> Z -12.188 11.060 23.248 11.528
> ****************************************************
> SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
> QM region + cutoff larger than box
> cannot continue, need larger box.
> Now the rst file show Box dimension: 28.9740000 23.0560000 27.7450000
> 90.0000000 90.0000000 90.0000000
> When I try to run calculation with cut and qmcut value of 8.0, the
> calculation even doesn't initiate. So to check if QM is applied to
> proper
> residues, I reduced the cut value to 4 (I referred to the mailing list
> letters for this). here the calculation begin which eventually ends
> after
> some 13000 steps.
> I tried to increase the box size by adding some methanol moelcules ( a
> box
> size around 70 70 70), still the same error appears.
> If the QM is applied to only oneresidue, the calculation runs smoothly,
> but
> not for two residues.
> How to work QMMM with QM on 2 residues?
> Please find attached all the needed files which were generated and
> point out
> mistake or suggestions to work out this problem
> Kaustubh

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Received on Thu Oct 06 2011 - 10:00:04 PDT
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