AMBER Archive (2007)

Subject: Re: AMBER: Fwd: QM region + cutoff larger that box

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Aug 04 2007 - 11:42:33 CDT

Bud:
Successful runs had qmmask=':1' while the problematic run had 1-2, as in
Tutorial A2. I though I copied the *.in files from the same location, where I
had edited to ':1'. Can't explain how the mistake arose. If no more posted,
this was the mistake. Thanks.

How did you check for convergence of PM3ESCF? As I posted before, this would
easy my tasks.

francesco pietra

--- "M. L. Dodson" <mldodson_at_houston.rr.com> wrote:

> To follow up to myself:
>
> M. L. Dodson wrote:
> > Francesco Pietra wrote:
> >> Although I suspected the problem does not arise from the box size, I
> >> have rerun
> >> md for the eq conformer. I started from prepin used successfully for
> >> the ax
> >> conformer in chcl3 and for both conformers in h2o. Setting the
> >> chloroform box
> >> 20A and md nstlim = 20,000.
> >>
> >> I have reexamined the min.in and md.in, they seem to be correct.
> >>
> >> It bombed at step 19150 with same indication "QM part + cutoff larger
> >> than
> >> box". As on previous runs, the mdcrd file shows the solute correctly
> >> immersed
> >> in molecules, allegedly chloroform. Say "allegedly" because of what said
> >> previously (below).
> >>
> >> Thanks
> >>
> >> francesco pietra
> >>
> >
> > Well, I've had a lot of practical experience recently with the
> > QMMM functionality, so let me give it a try.
> >
> > You say you did the run similarly to tutorial A2, but what is your
> > QM region definition? If you just copied the ':1-2' mask value of
> > the tutorial (first two residues), then the QM region probably
> > includes one of the solvent molecules. To follow up that
> > speculation, if that is what you did, then the QM CHCl3 is
> > diffusing away from the solute, moving out of the box.
> >
> > If your mask definition is equivalent to ':1' (i.e., just the
> > solute), then you must have cleaved your solute into two fragments
> > (not very likely). To get a QM region component to move out of
> > the QM box, the QM region must start with at least two components.
> >
>
> Actually, that may not be true. Depends on how the origin of the
> QM box is determined. If it is calculated once at the start of
> the run and not continually recentered, then it may be that your
> solute is just diffusing out of the box. This would not be seen
> with a QM region that consists of high MW solutes (at least in a
> normal run). Ross or Gustavo may have to referee this.
>
> > Please post your input file.
> >
>
> We still need this.
>
> > No help here on your VMD problem. My experience with VMD is that
> > it is very comprehensive and flexible, but you have to tell it
> > EXACTLY what you want to do if your problem is different from what
> > the VMD developers had in mind (and put that capability in the
> > menus). I.e., it is a programming language as much as a graphics
> > program.
> >
> > Bud Dodson
> >
> >>
> >> --- Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> >>
> >>> Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
> >>> From: Francesco Pietra <chiendarret_at_yahoo.com>
> >>> Subject: QM region + cutoff larger that box
> >>> To: Amber <amber_at_scripps.edu>
> >>>
> >>> QM-MM run successfully (20,000 steps) for axial methylcyclohexane in
> >>> chloroform
> >>> along the lines of Tutorial A2 with Amber9.
> >>>
> >>> Equatorial methylcyclohexane also run successfully for 10,000 steps.
> >>> When I
> >>> attemped to double nstlim (20,000), run bombed because QM region +
> >>> cutoff
> >>> (8.0)
> >>> larger than box (15.0). I repeated the run, instead of two
> >>> consecutive 10,000
> >>> steps, just a single run of 20,000 starting from where the
> >>> 10,000-step run
> >>> had
> >>> been successful. Same error bombing. out file for the latter run
> >>> attached. I
> >>> can't grasp where my error is.
> >>>
> >>> An additional query: I was unable to delete chloroform from VMD.
> >>> Curiously,
> >>> if
> >>> I indicate to show carbon only, this is shown correctly for the
> >>> methylcyclohexane molecule, while chloroform is shown as an ammonia-like
> >>> umbrella with four identical atoms. I.e., chlorine is shown as if it
> >>> were
> >>> carbon. Should I select a color for chlorine? I was unable to trace
> >>> where to
> >>> deal with chlorine atom. I used the chloroform box in Amber9.
> >>>
> >>> All that because I am checking convergence for ESCF with a simple test,
> >>> flexible molecule.
> >>>
> >>> Thanks
> >>>
> >>> francesco pietra
> >
>
> --
> M. L. Dodson
> Email: mldodson-at-houston-dot-rr-dot-com
> Phone: eight_three_two-five_63-386_one
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