<br>
Hi Sebastien,<br>
<br>
We meet again :)<br>
For a general tutorial on MD you can walk through the one at <a href="http://md.chem.rug.nl/education/mdcourse2004/">http://md.chem.rug.nl/education/mdcourse2004/</a><br>
There is another one specifically on setting up systems of a protein
and ligand, which may also be interesting to you, but for these I don't
know the sites.<br>
If you meet any problems directly related to the tutorial, you can also
contact me, as I'm for the greater part responsible for that site (and
I really need to revise it ;)).<br>
<br>
The 1-4 interaction either means that you have overlaps due to the
docking process which cause the system to explode, or a faulty
topology. If the latter is the case you would probably have had a 'long
bond' warning when running grompp.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 10/12/05, <b class="gmail_sendername">Erik Lindahl</b> <<a href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Sebastien,<span class="q"><div><br></div><div><br><div><div>On Oct 12, 2005, at 5:25 AM, Sebastien Gerega wrote:</div><br><blockquote type="cite"><div style="margin: 0px;">Hi all,</div><div style="margin: 0px;">I am pretty new to Gromacs and MDS in general... I am trying to run a simulation on a docked system (
<a href="http://www.members.optushome.com.au/sebkg/test.pdb" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.members.optushome.com.au/sebkg/test.pdb</a>)
and have tried several variations of what seem to be pretty standard
settings to me but when I go to run the EM I get the following:</div><div style="margin: 0px; min-height: 14px;"><br></div><div style="margin: 0px;">step 0 warning: 1-4 interaction between 725 and 730 at a distance 1.842
which is larger than the 1-4 table size 1.000 nm</div><div style="margin: 0px;">These are ignored for the rest of the simulation</div><div style="margin: 0px;">This usually means your system is exploding, if not, you should increase table-extension in your mdp file
</div><div style="margin: 0px;">Step 1 Warning: pressure scaling more than 1%, mu: 1.02036 1.02036 1.02036</div><div style="margin: 0px;">Segmentation fault</div></blockquote></div><font color="#0000dd"><br></font></div><div>
<font color="#0000dd"><br></font></div></span><div><font color="#0000dd">It's described in more detail here:</font></div><div><font color="#0000dd"><br></font></div><div><a href="http://www.gromacs.org/faq/index.php#1-4cut" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
http://www.gromacs.org/faq/index.php#1-4cut</a><font color="#0000dd"></font></div><div><br></div><div>Cheers,</div><span class="sg"><div><br></div><div>Erik</div><div><br></div>
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