<div dir="ltr">Hi all,<div><br></div><div>I think that this is properly within the scope of gmx development if Lorién believes there is some issue with the underlying code. I might suggest though that this is still not the right place for such discussions. If a minimal working example of the issue can be found, it should be posted on gitlab as a bug report. I think the confusion on where to post such issues is natural, since there are indeed a number of channels. This mailing list is mostly for low frequency anouncements, or for people seeking hints on how to get started on projects involving coding. As such, I think this was a reasonable enough place to ask for a small amount of insight, but that now the discussion should move to gitlab if there are further issues.</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, Feb 17, 2021 at 8:35 AM Bert de Groot <<a href="mailto:bgroot@gwdg.de">bgroot@gwdg.de</a>> wrote:<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 bgcolor="#FFFFFF">
Hi,<br>
<br>
This is not about gmx development, so gmx-developers is not the
appropriate channel.<br>
<br>
Lysozyme has multiple disulfide bonds (connecting cysteines), you
may be looking at one of those.<br>
<br>
Bert<br>
<br>
On 16/02/2021 17:18, Lorién López Villellas wrote:
<blockquote type="cite">
<div dir="ltr"><span><font color="#000000">Hello again.<br>
<br>
As Dmitry suggested, we have been working with the <i>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>iatoms</i> structure
(<i>idef->il[F_CONSTR].iatoms</i> in <i>Constraints::Impl::setConstraints()</i>).
We are currently testing our algorithm with the
GROMACS-Lysozime tutorial (the md-simulation part). The <i>elements_iatoms.txt</i> file attached contains <i>iatoms</i> and each atom element when calling to
setConstraints(). We see some weird bonds:<br>
</font>
<ul>
<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>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" target="_blank">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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