HI
I initially generated the one molar box , equilibrated it. The
phenol and imine residues were present randomly in the box. I used one set
of residues (22,23) to carry out umbrella sampling over the reaction
coordinate from 12 A to 2.25A. The rst structure I am using now for QMMM
calculation is one chosen from the MD simulation near the minima on that
reaction coordinate.
* Could you give guideline on how to set up QM region with these 2 residues
as one molecule? COuld you share some example?
* I tried iwrap=0 after your suggestion but that made no change.
* I got a suggestion to keep one of the molecules in the center (by using
some condition).Since other molecule is under constraint to be with in
2.6 A of the first, the system will stay in the center and this problem
(which possibly is occuring bcoz of one molecule crossing over the
boundary and reappearing from other side) can be overcome. But I could
not find any flag to do so. If you are aware plz. share.
* Could you give the link to prior thread you started.
Kaustubh
On Thu, Oct 6, 2011 at 5:02 PM, Brian Radak <radak004.umn.edu> wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
> --
> ================================ 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 - 09:00:03 PDT
