Marc
> How about putting a positional restraint (ntr=1) on ONE of your solute
> atoms?
> This should avoid diffusing of your solute.
>
> --Marc
Putting a position restraint on an atom should fix my problem.
But perhaps there are situations where the QM portion extends outside of the box without crashing sander (if qm_pme is not used like when using some external packages for forces)? I did not find any warning of the sort in the manual.
Thank You
Cody
>
> On 27 September 2015 at 21:49, Covington, Cody Lance <
> cody.l.covington.vanderbilt.edu> wrote:
>
> > Hello all
> >
> > During adQMMM calculations I am getting a box size error after many
> steps:
> > ....
> > NSTEP = 195200 TIME(PS) = 391.400 TEMP(K) = 297.25 PRESS =
> > 141.5
> > Etot = -19531.3004 EKtot = 4292.8913 EPtot =
> > -23824.1917
> > BOND = 3.6755 ANGLE = 19.8954 DIHED =
> > -0.7372
> > 1-4 NB = 4.5501 1-4 EEL = -0.1530 VDWAALS =
> > 3375.4160
> > EELEC = -25996.3407 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > PM6ESCF= -1230.4979
> > EKCMT = 2158.4788 VIRIAL = 1930.6103 VOLUME =
> > 74580.0076
> > Density =
> > 0.9702
> > Ewald error estimate: 0.2651E-01
> >
> > ----------------------------------------------------------------------
> > --------
> >
> > ****************************************************
> > ERROR: QM region + cutoff larger than box dimension:
> > QM-MM Cutoff = 7.0000
> > Coord Lower Upper Size Radius of largest sphere inside unit
> > cell
> > X -16.108 9.839 25.947 20.941
> > Y -13.744 10.130 23.874 20.941
> > Z -27.990 27.560 55.549 20.941
> > ****************************************************
> > SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f> QM
> region +
> > cutoff larger than box cannot continue, need larger box.
> >
> > I have noticed before that if part of the QM region is outside of the
> > box initially, it may not image some atoms properly and give this
> > error, so I centered my QM region to the center of the box before
> > running the MD. But now it seems my solute has diffused to the
> > periodic boundary during MD and is causing problems. Does anyone know
> of a way of fixing this?
> >
> > Thank You
> > Cody Covington
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Received on Mon Sep 28 2015 - 07:30:03 PDT
