<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Oct 3, 2013 at 5:21 PM, Floris van Eerden <span dir="ltr"><<a href="mailto:f.j.van.eerden@rug.nl" target="_blank">f.j.van.eerden@rug.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear reader,<br>
<br>
This post describes two different problems while I was trying to run a protein monomer.<br>
<br>
The first problem is that I get completely different results when I run a system with particle decomposition or domain decomposition.<br>
I simulate a coarse grained protein monomer embedded in a lipid bilayer and solvated in water+ions. When I use domain decomposition the system runs normal.<br>
However when I switch to particle dynamics the membrane starts buckling heavily, resulting in a completely folded membrane.<br></blockquote><div><br></div><div>Other than the range of non-bonded interactions, is there anything noteworthy in the topology or run setup? E.g. restraints, vsites, md-vv, replica exchange, free-energy... The most likely problem is some feature nobody ever tested / intended to work with PD. This is part of why PD is on the chopping block for 5.0.</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This is in Gromacs 4.5.5 and 4.5.3<br></blockquote><div><br></div><div>Please try a 4.5.7 run, so we can eliminate the years of accrued bug fixes as the source of the problem :-)</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I tried to reproduce these errors in Gromacs 4.6.3, but here my simulations kept crashing. When i used particle dynamics I get a lot of lincs warnings followed by a segmentation fault and when i use domain decomposition it crashes with a 'software inconsistency error: some particles seem to be assignment multipe times' (run on 8 cores with rdd set to 1.8). When I use only one thread (-n1 ) I get an segmentation fault. These while I can run these simulations without any problem (except the buckling) on gromacs 4.5.5. It does not matter if the tpr file is generated with gromacs 4.6.3 or gromacs 4.5.5.<br>
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Has anybody an idea what might be the problem?<br></blockquote><div><br></div><div>Some more information about your simulation would be good, but we'd probably like you to open an issue at <a href="http://redmine.gromacs.org">redmine.gromacs.org</a> so you can attach .tpr + preparation files as a tarball there.</div>
<div><br></div><div>Thanks!</div><div><br></div><div>Mark</div></div></div></div>