TJ Mustard wrote:
No this is a completely different error that occurs when the other (EM)
error does not.
So, EM completes, but you then get this unstable system? How well did EM
converge? Were the potential and maximum force acceptable?
Instabilities are generally caused by incorrect topologies or .mdp settings.
Those are the first places I would look for sources of error.
-Justin
Thank you,
TJ Mustard
On January 17, 2011 at 1:51 PM "Justin A. Lemkul" <[email protected]> wrote:
>
>
> TJ Mustard wrote:
> >
> >
> > Hi all,
> >
> >
> >
> > We have been running a lot of simulations on protein ligand
> > interactions, and my settings/setup/mdp files worked great for one
> > system. Then when we moved to a larger and more complicated system we
> > started getting mdrun 1-4 interaction errors in our MD.
> >
> >
> >
> > We are running with heavyh and have correctly made our ligands with
> > acpype and edited to have heavyh.
> >
> > Same setup as our smaller simpler model, but keep getting these:
> >
> >
> >
> > Warning: 1-4 interaction between X and Y at distance 1.804 which is
> > larger than 1-4 table size 1.800 nm.
> >
> >
> >
> > The jobs will continue on and finish but we are worried about the error
> > that could be included with these errors.
> >
> >
>
> Is this related to the other issue we're discussing? If so, please
do not
> double-post, especially if you're including different information in
different
> threads. It becomes a nightmare to try to keep track of.
>
> That particular error is usually not a good sign. Normal, stable
simulations
> should not give such an error.
>
> -Justin
>
> >
> >
> >
> > Any help would be appreciated. Also I can attach my mdp files.
> >
> >
> >
> > Thank you,
> >
> > TJ Mustard
> > Email: [email protected]
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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>
TJ Mustard
Email: [email protected]
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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