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><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">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>> Thanks Prof. David.<br>><br>> I've done all that now, but at the moment I'm locked getting lots of the<br>> "lovelly" error:<br>><br>> Warning: 1-4 interaction between 7 and 16 at distance
4.302 which is<br>> larger than the 1-4 table size 1.000 nm<br>> These are ignored for the rest of the simulation<br>> This usually means your system is exploding,<br>> if not, you should increase table-extension in your mdp file
<br>> step 0Segmentation fault<br><br>please give more details...<br><br><br>><br>> I've visually checked the .gro file, and the atoms mentioned are not<br>> from start at such crazy distances. I've included extra exclusions
<br>> between the virtual sites and the atoms that are at "one" and "two"<br>> "bonds" away.<br>><br>> Does it means I should include also the 1-4 in the exclusions or pair<br>> sections? Sorry, never dealt with dummy sites before this. I thought
<br>> using a pre-equilibrated box with a different model would at least avoid<br>> explosion problems, so or I missing something, of this assumption was<br>> completelly wrong.<br>><br>> Thanks a lot in advance,
<br>><br>> Sincerally yours<br>><br>> Jones<br>><br>> On 10/11/07, *David van der Spoel* <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><br>> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a>>> wrote:<br>><br>> Jones de Andrade wrote:<br>> > Hi all.<br>> ><br>> > Well, I'm having a bit of trouble here because the work has<br>> decided to
<br>> > go in the direction of something I've never used before with gromacs:<br>> > dummy atoms (or now "virtual sites").<br>><br>> I assume this is not for a protein, in which case pdb2gmx does it
<br>> for you.<br>> ><br>> > I've got at least three questions in order to use them:<br>> ><br>> > 1 - does the virtual sites need to be included in the .gro files in
<br>> > order to make a simulation run?<br>> ><br>> Yes.<br>><br>> > 2 - do I need to include them in the "exclusion list"?<br>> It depends, but usually yes.<br>
><br>> ><br>> > 3 - do I need to include them in the "atoms" section?<br>> Yes.<br>><br>> ><br>> ><br>> > Thanks a lot in advance for any help anyone can provide in these
<br>> > subjects. ;)<br>> Check the mannual too. Chapter 5. An dtopologies for TIP4P, TIP5P etc.<br>><br>><br>> ><br>> > Sincerally yours,<br>> ><br>> > Jones
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</a><br><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.<br><a href="mailto:spoel@xray.bmc.uu.se">
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