AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat Aug 04 2007 - 09:33:35 CDT

Problems with VMD/chlorine clarified.

As to my difficulties with QM-MM runs with chloroform box (as indicated below)
I should point out that Ewald error is ca 0.4E-01 with the water box, where
everything
 runs perfectly), while with the problematic chloroform box the error rises to
ca 0.7E+01.

francesco pietra

--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Sat, 4 Aug 2007 01:32:40 -0700 (PDT)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Fwd: QM region + cutoff larger that box
> To: Amber <amber_at_scripps.edu>
>
> 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
>
>
> --- 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
> >
> >
> >
> >
>
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