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.yahoo.com> wrote:
> Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
> From: Francesco Pietra <chiendarret.yahoo.com>
> Subject: QM region + cutoff larger that box
> To: Amber <amber.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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Received on Sun Aug 05 2007 - 06:08:04 PDT
