<p dir="ltr">Sorry, I meant "can be easily done already," not "is done." The infrastructure to chain a few gromacs tools as in a shell script is now there, it's just not yet used much yet.</p>
<p dir="ltr">Mark</p>
<div class="gmail_quote">On Dec 17, 2013 2:52 PM, "Alexey Shvetsov" <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mark Abraham писал 17-12-2013 06:35:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
"Does not segfault" is easily done already with the integration test<br>
machinery recently added. Anything more sophisticated needs a way to<br>
examine the results and compare with what was expected...<br>
</blockquote>
<br>
It wasnt. For example genbox doesnt work in 5.0-beta1 it segfaults, and tests doesnt cover it<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Mark<br>
On Dec 17, 2013 2:51 AM, "Szilárd Páll" <<a href="mailto:pall.szilard@gmail.com" target="_blank">pall.szilard@gmail.com</a>><br>
wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I agree, there is value in such a test even if it is used to only<br>
check that the tools used work. Of course, providing somewhat<br>
stricter<br>
checks on what "works" mean should be the goal, but even if the<br>
first<br>
version does not do this, I suggest adding such a test.<br>
<br>
Cheers,<br>
--<br>
Szilárd<br>
<br>
On Mon, Dec 16, 2013 at 3:05 PM, Alexey Shvetsov<br>
<<a href="mailto:alexxy@omrb.pnpi.spb.ru" target="_blank">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin Lemkul писал 16-12-2013 17:34:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Mon, Dec 16, 2013 at 5:34 AM, Alexey Shvetsov<br>
<<a href="mailto:alexxy@omrb.pnpi.spb.ru" target="_blank">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi!<br>
<br>
May be it will be good to have small test that emulates full<br>
</blockquote></blockquote></blockquote>
cycle<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
of md system preparation and run (just for few dozens of steps<br>
</blockquote></blockquote></blockquote>
for<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
each mdrun). As small peptide we can use e.g. speptide,<br>
</blockquote></blockquote></blockquote>
cpeptide or<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
may be even trp-cage. This will allow to catch bugs in<br>
</blockquote></blockquote></blockquote>
preparation<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
utils (e.g. genbox, genion)<br>
</blockquote>
<br>
<br>
That could be good, but how robust would such a test be?<br>
</blockquote></blockquote>
Energies<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
could vary quite a bit based on ion placement (which by default<br>
</blockquote></blockquote>
is<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
random) and I have even seen cases where genbox adds a slightly<br>
different number of waters to identical solutes in identical<br>
</blockquote></blockquote>
boxes, so<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
the topology may not even be consistent. This is fairly rare,<br>
</blockquote></blockquote>
but I<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
do get people panicking when doing my tutorials if they somehow<br>
</blockquote></blockquote>
get<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
one fewer water molecule in their box ;)<br>
<br>
</blockquote>
<br>
I think it will be test to check it all tools works as expected<br>
</blockquote>
without<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
crashes and segfaults.<br>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
-Justin<br>
<br>
--<br>
<br>
==============================<u></u>============<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Postdoctoral Fellow<br>
<br>
Department of Pharmaceutical Sciences<br>
School of Pharmacy<br>
Health Sciences Facility II, Room 601<br>
University of Maryland, Baltimore<br>
20 Penn St.<br>
Baltimore, MD 21201<br>
<br>
<a href="mailto:jalemkul@outerbanks.umaryland.edu" target="_blank">jalemkul@outerbanks.umaryland.<u></u>edu</a> | (410) 706-7441<br>
<br>
==============================<u></u>============<br>
</blockquote>
<br>
<br>
--<br>
Best Regards,<br>
Alexey 'Alexxy' Shvetsov<br>
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,<br>
</blockquote>
Gatchina,<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Russia<br>
Department of Molecular and Radiation Biophysics<br>
Gentoo Team Ru<br>
Gentoo Linux Dev<br>
mailto:<a href="mailto:alexxyum@gmail.com" target="_blank">alexxyum@gmail.com</a><br>
mailto:<a href="mailto:alexxy@gentoo.org" target="_blank">alexxy@gentoo.org</a><br>
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Department of Molecular and Radiation Biophysics<br>
Gentoo Team Ru<br>
Gentoo Linux Dev<br>
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