<div dir="ltr">Wow! I never got around to analysing the <font face="monospace">-rerun</font> argument. Let me process this one. <div>Thank you!</div></div><br><div class="gmail_quote"><div dir="ltr">On Mon, Feb 5, 2018 at 3:19 PM Justin Lemkul &lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt; wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div text="#000000" bgcolor="#FFFFFF">
    <br>
    <br>
    <div class="m_3705472701366429378moz-cite-prefix">On 2/5/18 3:15 PM, Sanyam Kapoor wrote:<br>
    </div>
    <blockquote type="cite">
      <div dir="ltr">Hello everyone,
        <div><br>
        </div>
        <div>I&#39;ve been trying to familiarize myself with the Gromacs
          codebase over the past couple weeks and have figured out
          various control flows.</div>
        <div><br>
        </div>
        <div>My question is in reference to the energy minimization step
          via &quot;<font face="monospace">do_steep</font>&quot;, which calls &quot;<span style="font-size:9pt"><font face="monospace">evaluate_energy</font></span>&quot;.
          Am I correct in understanding that this is the only function
          which calculates the potential energy of a topology state? It
          appears that this function is very tightly coupled with the
          multi-threading system and hence the concern.</div>
        <div><br>
        </div>
        <div>My aim is to build a C wrapper around this function but
          that will only be possible if I can get a bare bones energy
          estimator from the topology.</div>
        <div><br>
        </div>
        <div>Apologies for any technically incorrect statement, I don&#39;t
          actually have a Molecular Dynamics background.</div>
        <div><br>
        </div>
      </div>
    </blockquote>
    <br></div><div text="#000000" bgcolor="#FFFFFF">
    You should not invoke the energy minimizer at all. The process you
    want to carry out is best done with mdrun -rerun and a .tpr file
    that specifies zero MD steps:<br>
    <br>
    <a class="m_3705472701366429378moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy" target="_blank">http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy</a><br>
    <br>
    -Justin<br>
    <pre class="m_3705472701366429378moz-signature" cols="72">-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

<a class="m_3705472701366429378moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> | <a href="tel:(540)%20231-3129" value="+15402313129" target="_blank">(540) 231-3129</a>
<a class="m_3705472701366429378moz-txt-link-freetext" href="http://www.biochem.vt.edu/people/faculty/JustinLemkul.html" target="_blank">http://www.biochem.vt.edu/people/faculty/JustinLemkul.html</a>

==================================================
</pre>
  </div>

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<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" rel="noreferrer" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" target="_blank">gmx-developers-request@gromacs.org</a>.</blockquote></div>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature">Regards,<br>Sanyam Kapoor<br>Masters in Computer Science<br>Courant Institute, New York University<br><a href="https://www.sanyamkapoor.com">https://www.sanyamkapoor.com</a></div>