<div dir="ltr"><span class="gmail-im" style=""><font color="#000000" style="">Hello again.<br><br>As Dmitry suggested, we have been working with the <i style="">gmx_mtop_t</i> data. So far, it seems that it is what we needed.<br><br>However, we are having some trouble with the <i style="">iatoms</i> structure (<i style="">idef->il[F_CONSTR].iatoms</i> in <i style="">Constraints::Impl::setConstraints()</i>). We are currently testing our algorithm with the GROMACS-Lysozime tutorial (the md-simulation part). The <i style="">elements_iatoms.txt</i> file attached contains <i style="">iatoms</i> and each atom element when calling to setConstraints(). We see some weird bonds:<br></font><ul style=""><li style="margin-left:15px"><font color="#000000">Bond 1938, which is part of a cysteine amino acid (let us call it amino acid x), connects atom 1910 (carbon) with atom 1913 (sulfur), forming a C-S bond, which is just right.</font></li><li style="margin-left:15px"><font color="#000000">Bond 100, connects atom 98 (sulfur) with atom 1913 (the sulfur atom of amino acid x). As far as I know, a connection S-S is not even possible in a peptide-chain.</font></li><li style="margin-left:15px"><font color="#000000">The bond that should connect atom 1913 with a hydrogen atom does not exist.</font></li></ul></span><font color="#000000"><span class="gmail-im" style="">What is weird is that almost every bond makes sense, except some bonds like the ones shown below. As this structure is used in SHAKE, I guess we are doing something wrong.<br><br>Thank you all in advance.<br><br></span>Regards,<br>Lorién</font><br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue, 11 feb 2021 a las 19:16, Lorién López Villellas (<<a href="mailto:lorien.lopez@bsc.es">lorien.lopez@bsc.es</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi.<br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">One the possible solutions (there are atomic numbers stored in the gmx_mtop_t)</blockquote><div> </div><div>I think we can work with that. Thanks!<br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">But that would make the algorithm work only for proteins. Why not do the numbering based on bond connectivity?</blockquote><br>We have two versions of the algorithm, a sequential one that works with any molecule and a parallel one that, as you say, only works with proteins. The parallelization of the algorithm is based on the structure of the peptide chain. The numbering we use is extremely specific; each amino acid bond must always have the same index. The reordering algorithm needs to identify each of the molecule bonds precisely. We have not found a way to achieve that without using the additional information that the atoms' element provides.<br><br>Regards,<br>Lorién<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue, 11 feb 2021 a las 17:30, Berk Hess (<<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>On 2/11/21 4:22 PM, Lorién López
Villellas wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi.<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Why
is the element number relevant for constraints? The element
number is never used in MD calculations.</blockquote>
<br>
We have performed a heavy code optimization based on the
structural patterns of the peptide chains. In order to apply
this optimization, we need a very specific bond numbering. To
get to this bond numbering, we use a bond reordering phase. The
reordering algorithm needs to know the elements of the
molecule's atoms to locate itself.<br>
<br>
</div>
</blockquote>
But that would make the algorithm work only for proteins. Why not do
the numbering based on bond connectivity?<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
</div>
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