Kaustubh,
Are the 2 residues wrapping differently? It looks like parts of your QM
region might be on opposite sides of the cell (large negative and positive
coordinates in the lower/upper columns). I think, but am not sure, that
using iwrap = 0 would solve that problem.
In my QM/MM simulations I usually try to set the QM region as one molecule
in the prmtop so that it always images together. This requires that all of
the atoms be bonded together, even if those bonded terms are never used,
which is the default behavior for QM/MM anyway. This might also require
creating an frcmod with non-standard bonded terms (they can just have 0
force constant if you'd like also).
I also started a thread several weeks ago while experiencing a similar
problem that seemed to be caused by a non-orthorhombic cell. I see that you
are using orthorhombic conditions, but that discussion might also be of
interest.
Regards,
Brian
On Thu, Oct 6, 2011 at 10:46 AM, kaustubh joshi <kandrjoshi.gmail.com>wrote:
> 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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>
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Thu Oct 06 2011 - 08:30:02 PDT
