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<p style="margin: 0px;"><span>No this is a completely different error that occurs when the other (EM) error does not.</span></p>
<p style="margin: 0px;"><span> </span></p>
<p style="margin: 0px;"><span>Thank you,</span></p>
<p style="margin: 0px;"><span>TJ Mustard<br />
</span></p>
<div style="margin: 5px 0px 5px 0px;">
On January 17, 2011 at 1:51 PM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> ><br />
> > Hi all,<br />
> ><br />
> > <br />
> ><br />
> > We have been running a lot of simulations on protein ligand<br />
> > interactions, and my settings/setup/mdp files worked great for one<br />
> > system. Then when we moved to a larger and more complicated system we<br />
> > started getting mdrun 1-4 interaction errors in our MD.<br />
> ><br />
> > <br />
> ><br />
> > We are running with heavyh and have correctly made our ligands with<br />
> > acpype and edited to have heavyh.<br />
> ><br />
> > Same setup as our smaller simpler model, but keep getting these:<br />
> ><br />
> > <br />
> ><br />
> > Warning: 1-4 interaction between X and Y at distance 1.804 which is<br />
> > larger than 1-4 table size 1.800 nm.<br />
> ><br />
> > <br />
> ><br />
> > The jobs will continue on and finish but we are worried about the error<br />
> > that could be included with these errors.<br />
> ><br />
> > <br />
><br />
> Is this related to the other issue we're discussing?  If so, please do not<br />
> double-post, especially if you're including different information in different<br />
> threads.  It becomes a nightmare to try to keep track of.<br />
><br />
> That particular error is usually not a good sign.  Normal, stable simulations<br />
> should not give such an error.<br />
><br />
> -Justin<br />
><br />
> ><br />
> > <br />
> ><br />
> > Any help would be appreciated. Also I can attach my mdp files.<br />
> ><br />
> > <br />
> ><br />
> > Thank you,<br />
> ><br />
> > TJ Mustard<br />
> > Email: mustardt@onid.orst.edu<br />
> ><br />
><br />
> --<br />
> ========================================<br />
><br />
> Justin A. Lemkul<br />
> Ph.D. Candidate<br />
> ICTAS Doctoral Scholar<br />
> MILES-IGERT Trainee<br />
> Department of Biochemistry<br />
> Virginia Tech<br />
> Blacksburg, VA<br />
> jalemkul[at]vt.edu | (540) 231-9080<br />
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br />
><br />
> ========================================<br />
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</div>
<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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