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Sounds dangerous to me. Here's a possible methods section from your paper:
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<div>"we obtained a popc bilayer somewhere on the internet. Unfortunately, this structure did not match our topology file. Nevertheless, it has the same number of atoms and so we assumed that the difference was simply a matter of reordering ..." (not too appealing
I think).</div>
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<div>Peter's advice was good and I recommend avoiding a reordering based on an assumption that it will be correct. Using the method that Peter outlined, there will be some issues with equilibration at the new periodic boundary, but 100 ns of MD simulation should
take care of that just fine (note that the Tieleman 128 lipid file is pretty old and, computers being slower then, I imagine that it was equilibrated with fewer than 100 ns itself).</div>
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<div>Chris.</div>
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<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">On 2012-05-28 08:03, James Starlight wrote:</span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> Peter,</span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">></span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> Thanks for advise.</span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">></span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> I've found already pre-equilibrated POPC bilayers with 200 lipids. </span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> I've examined that lipids and found that they are very similar to the </span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> berger's lipids (it consists of equal nymber of atoms ) but the atom </span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> order in each lipid is slightly different than in Tieleman's popc.itp </span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> file so during processing of that lipids I've got error of </span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> non-matching atoms. Is there any trivial way to make new popc.itp </span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> based on existing gro file with correct atom order ?</span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">></span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">></span><br style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">
<span style="font-family: 'Segoe UI', Helvetica, Arial, sans-serif; font-size: 13px; ">> James</span>
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