<div dir="ltr">Hi,<div><br></div><div>Sounds like we should look into that. Can you share a tarball of inputs, or at least a tpr, on a new redmine, please?</div><div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Sun, May 14, 2017 at 10:58 PM Vedran Miletić <<a href="mailto:vedran@miletic.net">vedran@miletic.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello Berk, others,<br>
<br>
I observed a regression which results in mdrun NVT or production MD<br>
crashing under certain conditions and bisected it to 5b88d3c18 Remove<br>
state duplication in serial runs. The minimal example is that causes<br>
this is ACACACA peptide (easy to generate with e.g. PyMOL) running EM<br>
and MD with Justin's mdp files [1, 2] using the following sequence of<br>
commands:<br>
<br>
gmx pdb2gmx -f acacaca.pdb -ignh<br>
gmx editconf -f conf.gro -o conf_newbox.gro -c -d 1.0 -bt cubic<br>
gmx solvate -cp conf_newbox.gro -cs spc216.gro -o conf_solv.gro -p topol.top<br>
gmx grompp -f minim.mdp -c conf_solv.gro -p topol.top -o em.tpr<br>
gmx mdrun -deffnm em -v<br>
gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr<br>
gmx mdrun -deffnm md -v<br>
<br>
Prior to 5b88d3c18 this will run fine, but 5b88d3c18 and later revisions<br>
result in<br>
<br>
step 0<br>
Step 1, time 0.002 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 113.755112, max 983.434143 (between atoms 38 and 39)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
22 24 48.4 0.1336 0.2057 0.1335<br>
24 25 50.6 0.1010 0.1576 0.1010<br>
24 26 87.9 0.1450 0.3411 0.1449<br>
26 27 85.5 0.1090 0.2146 0.1090<br>
26 28 76.3 0.1526 0.2979 0.1526<br>
26 32 80.4 0.1524 0.4376 0.1522<br>
28 29 50.7 0.1089 0.1687 0.1090<br>
28 30 54.4 0.1094 0.1528 0.1090<br>
28 31 52.0 0.1089 0.1709 0.1090<br>
32 33 82.8 0.1230 0.2838 0.1229<br>
32 34 149.8 0.1337 4.0620 0.1335<br>
34 35 104.7 0.1011 4.0236 0.1010<br>
36 37 87.6 0.1091 0.1962 0.1090<br>
36 38 94.4 0.1524 0.5549 0.1526<br>
36 43 91.1 0.1524 0.6512 0.1522<br>
38 39 122.4 0.1992 107.3033 0.1090<br>
38 40 91.5 0.1085 0.1488 0.1090<br>
38 41 73.0 0.1806 0.0914 0.1810<br>
43 44 33.7 0.1230 0.0828 0.1229<br>
Segmentation fault<br>
<br>
Since this particular revision did not change mdp settings, I presume<br>
MDP files from Justin's tutorial are fine.<br>
<br>
Regards,<br>
Vedran<br>
<br>
[1]<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp" rel="noreferrer" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp</a><br>
[2]<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp" rel="noreferrer" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp</a><br>
<br>
--<br>
Vedran Miletić<br>
<a href="http://vedran.miletic.net" rel="noreferrer" target="_blank">vedran.miletic.net</a><br>
--<br>
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