AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Aug 16 2009 - 11:55:01 CDT

I think you will find that Prof. Case's main point was not to use Divcon
(idc=1) for the QM/MM. I concur with him here. Rather than messing around
with different and complex minimisation settings which will just serve to
confuse the matter I would suggest switching to the internal QM/MM (idc=0)
and then seeing what happens. If you still have problems please post the
output to the list and I will take a look.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Ashish Runthala
> Sent: Friday, August 14, 2009 11:43 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Strange QM/MM Divcon - help me out
>
> Ya
> 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 <case_at_biomaps.rutgers.edu> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Ashish Runthala,
> Faculty Division III,
> Assistant Lecturer, Biological Sciences,
> Birla Institute of Technology and Science,
> Pilani, Rajasthan- 333031
> INDIA
>
> _______________________________________________
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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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