<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Dec 16, 2013 at 5:34 AM, Alexey Shvetsov <span dir="ltr"><<a href="mailto:alexxy@omrb.pnpi.spb.ru" target="_blank">alexxy@omrb.pnpi.spb.ru</a>></span> wrote:<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 cycle of md system preparation and run (just for few dozens of steps for each mdrun). As small peptide we can use e.g. speptide, cpeptide or may be even trp-cage. This will allow to catch bugs in preparation utils (e.g. genbox, genion)<span class="HOEnZb"><font color="#888888"><br>
<br></font></span></blockquote><div><br></div><div style>That could be good, but how robust would such a test be? Energies could vary quite a bit based on ion placement (which by default is random) and I have even seen cases where genbox adds a slightly different number of waters to identical solutes in identical boxes, so the topology may not even be consistent. This is fairly rare, but I do get people panicking when doing my tutorials if they somehow get one fewer water molecule in their box ;)</div>
<div style><br></div><div style>-Justin</div><div><br></div><div>-- <br></div></div><div dir="ltr"><span style="font-family:arial,helvetica,sans-serif"></span><pre><span style="font-family:arial,helvetica,sans-serif">==========================================
Justin A. Lemkul, Ph.D.
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></span></pre><pre>
<span style="font-family:arial,helvetica,sans-serif"><a href="mailto:jalemkul@outerbanks.umaryland.edu" target="_blank">jalemkul@outerbanks.umaryland.edu</a> | (410) 706-7441<br></span></pre><pre><span style="font-family:arial,helvetica,sans-serif"><br>
==========================================</span></pre><br></div>
</div></div>