AMBER Archive (2009)

Subject: Re: [AMBER] Strange QM/MM Divcon - help me out

From: Ashish Runthala (
Date: Sat Aug 15 2009 - 01:42:38 CDT

Prof case is right about that.
Better run a smaller simulation specifying the cycles.
Better use ntmin=2, for your simulation. If it doesn't fix the
problem. do a smaller simulation.

On 8/13/09, case <> wrote:
> On Thu, Aug 13, 2009, s. Bill wrote:
>> I was trying to do simulation of a solvated protein using QM/MM
>> DivCon.
> Just a question: are you sure you want to do this? It looks like your
> quantum region is only 11 atoms. There is no advantage to using divcon, and
> you should remember that it has been tested by fewer people than the
> non-divcon
> QM/MM code. Plus, options like qm_pme and qm_ewald are ignored by divcon,
> which may not be what you want.
>> atoms, and after 3ps it stopped, becuase a part of the protein moving
>> away.
> You probably need to run a simulation slightly shorter than the one that
> crashes, then look at the output coordinates visually, and start to figure
> out
> what is happening.
> ...dac
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Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031

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