Hi all.<br><br>Just informing, I tried a single molecule, and the topology with all dummies minimize (despite taking loads of steps bfgs steps).<br><br>The interesting thing is that the distance between atom 6 and 17 at beggining reads
3.1 angstrons, and at the end read 2.9 angstrons.<br><br>Why it's going bad with many molecules or even single molecule MD, God?<br><br>Thanks a lot everybody in advance,<br><br>Sincerally yours,<br><br>Jones<br><br><div>
<span class="gmail_quote">On 10/11/07, <b class="gmail_sendername">Jones de Andrade</b> <<a href="mailto:johannesrs@gmail.com">johannesrs@gmail.com</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 Prof. David.<br><br>Yes, it a self created topology. This one is based on another self created topology that runs perfectly for cyclohexane. It was adapted to include the dummy atoms.<br><br>I guess there is something wrong in the definition of the dummies in the topology. But I have no clue where it is. Can you provide me some clue on this?
<br><br>I'll run a single molecule now.<span class="q"><br><br>Thanks a lot in advance,<br><br>Sincerally yours,<br><br>Jones<br><br></span><div><span class="e" id="q_1158ffafd0e56e65_2"><div><span class="gmail_quote">
On 10/11/07, <b class="gmail_sendername">David van der Spoel</b> <
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">spoel@xray.bmc.uu.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;">
Jones de Andrade wrote:
<br>> Hi Prof. David.<br>><br>> What details do you mean? Actual topology files are attached. Anything else?<br>><br>> Thanks a lot in advance!<br>><br>> Sincerally yours,<br>><br>> Jones<br>>
<br>There is something wrong in the topology, youäll have to debug it<br>yourself...<br><br>--<br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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