AMBER: Fwd: QM region + cutoff larger that box

From: Francesco Pietra <>
Date: Sat, 4 Aug 2007 01:32:40 -0700 (PDT)

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 and, 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).


francesco pietra

--- Francesco Pietra <> wrote:

> Date: Fri, 3 Aug 2007 10:02:35 -0700 (PDT)
> From: Francesco Pietra <>
> Subject: QM region + cutoff larger that box
> To: Amber <>
> 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
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