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    <div class="moz-cite-prefix">On 1/4/18 4:55 AM, Mark Abraham wrote:<br>
    </div>
    <blockquote type="cite"
cite="mid:CAMNuMASLJK=JpBvJ7HtubFKw4H2Nb+ULzy6iOS7KwHwXX9se=g@mail.gmail.com">
      <div dir="ltr">Hi,<br>
        <br>
        <div class="gmail_quote">
          <div dir="ltr">On Thu, Jan 4, 2018 at 10:36 AM Jernej Zidar
            &lt;<a href="mailto:jernej.zidar@gmail.com"
              moz-do-not-send="true">jernej.zidar@gmail.com</a>&gt;
            wrote:<br>
          </div>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">Hi,
              <div><br>
              </div>
              <div>The "-deffnm" option is very handy because the user
                doesn't have to specify every single output file
                (energy, trajectory, log, checkpoint).</div>
            </div>
          </blockquote>
          <div><br>
          </div>
          <div>But what's the requirement for renaming them? The default
            names are fine - name collisions only arise when someone
            tries to do their entire (sub)project in the same directory,
            which IMO is an anti-pattern.</div>
        </div>
      </div>
    </blockquote>
    <br>
    To counter that, I train my students to ALWAYS use descriptive file
    names. Of course one can have a variety of organizational schemes,
    but training someone who is new to MD is difficult if they just have
    a lot of generically named files, because a lot of the initial
    concepts are somewhat abstract. <br>
    <br>
    "What's in traj.trr?" (student gives blank stare)<br>
    "What's in md_20_30.trr?" (student says "the trajectory data from
    20-30 ns")<br>
    <br>
    The connection is obvious in how one assembles proper inputs and
    uses previous output to move forward.<br>
    <br>
    I, for one, would HATE to lose -deffnm. It's going to make teaching
    new users more difficult and it's going to break every script I
    have.<br>
    <br>
    -Justin<br>
    <br>
    <blockquote type="cite"
cite="mid:CAMNuMASLJK=JpBvJ7HtubFKw4H2Nb+ULzy6iOS7KwHwXX9se=g@mail.gmail.com">
      <div dir="ltr">
        <div class="gmail_quote">
          <div> </div>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">
              <div>This option should be kept if it is not too much
                trouble.</div>
            </div>
          </blockquote>
          <div><br>
          </div>
          <div>The trouble is not the simple case, where it works fine.
            The trouble is the forest of files that get written by all
            the modules. There's a lot of infrastructure (and test
            cases) needed so that all combinations of e.g. mdrun -deffnm
            -multi -px -append work reliably, now, and under
            maintenance.</div>
          <div><br>
          </div>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">
              <div>Personally, I'd like to see this option applied to
                other tools as well (trjconv for example).</div>
            </div>
          </blockquote>
          <div><br>
          </div>
          <div>What's an example use case, please?</div>
          <div><br>
          </div>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">
              <div>One suggestion: Would it be possible to have all the
                tools that analyze trajectories aware of the "-tu"
                switch ? It's way more convenient to specify the time in
                ns, ms, ... than in number of steps. </div>
            </div>
          </blockquote>
          <div><br>
          </div>
          <div>Maybe, but perhaps you are referring to -b and -t (which
            take input in ps, not steps). Again, there's a lot of
            infrastructure and testing needed to make that work (and
            potentially confusing if any other time-related option is
            not also similarly customizable). We've historically done a
            poor job of that, and now have about as much debt as
            assets... I don't see enough value in </div>
          <div><br>
          </div>
          <div>gmx tool -tu ns -b 10 -e 20</div>
          <div><br>
          </div>
          <div>vs</div>
          <div><br>
          </div>
          <div>gmx tool -b 10000 -e 20000</div>
          <div><br>
          </div>
          <div>for someone to want to put their time into it.</div>
          <div><br>
          </div>
          <div>Mark</div>
          <div> </div>
          <blockquote class="gmail_quote" style="margin:0 0 0
            .8ex;border-left:1px #ccc solid;padding-left:1ex">
            <div dir="ltr">
              <div><br>
              </div>
              <div>Comments?</div>
              <div> </div>
              <div>Cheers,</div>
              <div>Jernej Zidar</div>
            </div>
            <div dir="ltr">
              <div><br>
                <div class="gmail_extra"><br>
                  <div class="gmail_quote">On Thu, Jan 4, 2018 at 5:15
                    PM, Mark Abraham <span dir="ltr">&lt;<a
                        href="mailto:mark.j.abraham@gmail.com"
                        target="_blank" moz-do-not-send="true">mark.j.abraham@gmail.com</a>&gt;</span>
                    wrote:<br>
                    <blockquote class="gmail_quote" style="margin:0 0 0
                      .8ex;border-left:1px #ccc solid;padding-left:1ex">
                      <div dir="ltr"><br>
                        <div>We should also be aware that -deffnm is
                          brittle in the same way that -multi is,
                          because our filename-handling machinery
                          doesn't centralize changing the prefix/suffix
                          needed to support -deffnm or -multi. So I
                          think we should plan to announce -deffnm as
                          deprecated in the 2019 release (and remove
                          after that). If we think that's useful enough
                          to want to keep, we need people to put up
                          their hands for the work to make all the mdrun
                          modules work with it.<br>
                        </div>
                        <div><br>
                        </div>
                        <div>Thanks,</div>
                        <div><br>
                        </div>
                        <div>Mark</div>
                      </div>
                      <br>
                    </blockquote>
                  </div>
                </div>
              </div>
            </div>
            --<br>
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    <pre class="moz-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="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-3129
<a class="moz-txt-link-freetext" href="http://www.biochem.vt.edu/people/faculty/JustinLemkul.html">http://www.biochem.vt.edu/people/faculty/JustinLemkul.html</a>

==================================================
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