<div style="font-size: 12pt; font-family: Calibri,sans-serif;">Hi,<div><br></div><div>Since with the Verlet scheme charge groups are single atoms, this error is correct. But some more explanation could be useful.</div><div><br></div><div>Cheers,</div><div><br></div><div>Berk</div><br><div id="htc_header">----- Reply message -----<br>From: "Szilárd Páll" <pall.szilard@gmail.com><br>To: "Discussion list for GROMACS development" <gmx-developers@gromacs.org><br>Subject: [gmx-developers] strange SHAKE + Verlet scheme warning?<br>Date: Fri, May 2, 2014 17:25</div></div><br><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div><span style="font-family:arial,sans-serif;font-size:13px">Hi,</span><div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I've come across a somewhat strange issue and I thought I'd ask before filing a redmine - especially as I'm not sure whether this is only a documentation/code self-documentation bug or a buggy behavior too.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">I'm running 5.0 RC1 (git), Verlet scheme with a small water box of ~500 molecules and -DFLEXIBLE with SHAKE constraints. </div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Trying to start a DD run I get this error:</div><div style="font-family:arial,sans-serif;font-size:13px">
<br></div><div style="font-family:arial,sans-serif;font-size:13px"><div><div>-------------------------------------------------------</div><div>Program mdrun_d, VERSION 5.0-rc1-dev-20140430-81378bd</div><div>Source code file: /home/pszilard/projects/gromacs/gromacs-5.0/src/gromacs/mdlib/constr.c, line: 1266</div>
<div><br></div><div>Fatal error:</div><div>SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS</div><div>For more information and tips for troubleshooting, please check the GROMACS</div>
<div>website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a></div><div>-------------------------------------------------------</div></div><div><br></div>
</div><div style="font-family:arial,sans-serif;font-size:13px">Now, this is inconsistent at least with the fact that charge groups are removed by grompp with the Verlet scheme. The documentation does point out that "SHAKE does not support constraints between atoms on different nodes", though.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Looking a the code, the bInterCGcons that triggers it still refers to charge groups, so there is definitely room for improvement both in error message, variable naming, as well as documentation.</div>
<div style="font-family:arial,sans-serif;font-size:13px"><br></div><div style="font-family:arial,sans-serif;font-size:13px">Cheers,</div><div style="font-family:arial,sans-serif;font-size:13px">--<br>Szilárd</div>
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