[gmx-developers] Regression since 5b88d3c18 Remove state duplication in serial runs

[Mark Abraham]

Hi,

Sounds like we should look into that. Can you share a tarball of inputs, or
at least a tpr, on a new redmine, please?

Mark

On Sun, May 14, 2017 at 10:58 PM Vedran Miletić <vedran at miletic.net> wrote:

> Hello Berk, others,
>
> I observed a regression which results in mdrun NVT or production MD
> crashing under certain conditions and bisected it to 5b88d3c18 Remove
> state duplication in serial runs. The minimal example is that causes
> this is ACACACA peptide (easy to generate with e.g. PyMOL) running EM
> and MD with Justin's mdp files [1, 2] using the following sequence of
> commands:
>
> gmx pdb2gmx -f acacaca.pdb -ignh
> gmx editconf -f conf.gro -o conf_newbox.gro -c -d 1.0 -bt cubic
> gmx solvate -cp conf_newbox.gro -cs spc216.gro -o conf_solv.gro -p
> topol.top
> gmx grompp -f minim.mdp -c conf_solv.gro -p topol.top -o em.tpr
> gmx mdrun -deffnm em -v
> gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr
> gmx mdrun -deffnm md -v
>
> Prior to 5b88d3c18 this will run fine, but 5b88d3c18 and later revisions
> result in
>
> step 0
> Step 1, time 0.002 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 113.755112, max 983.434143 (between atoms 38 and 39)
> bonds that rotated more than 30 degrees:
>   atom 1 atom 2  angle  previous, current, constraint length
>       22     24   48.4    0.1336   0.2057      0.1335
>       24     25   50.6    0.1010   0.1576      0.1010
>       24     26   87.9    0.1450   0.3411      0.1449
>       26     27   85.5    0.1090   0.2146      0.1090
>       26     28   76.3    0.1526   0.2979      0.1526
>       26     32   80.4    0.1524   0.4376      0.1522
>       28     29   50.7    0.1089   0.1687      0.1090
>       28     30   54.4    0.1094   0.1528      0.1090
>       28     31   52.0    0.1089   0.1709      0.1090
>       32     33   82.8    0.1230   0.2838      0.1229
>       32     34  149.8    0.1337   4.0620      0.1335
>       34     35  104.7    0.1011   4.0236      0.1010
>       36     37   87.6    0.1091   0.1962      0.1090
>       36     38   94.4    0.1524   0.5549      0.1526
>       36     43   91.1    0.1524   0.6512      0.1522
>       38     39  122.4    0.1992 107.3033      0.1090
>       38     40   91.5    0.1085   0.1488      0.1090
>       38     41   73.0    0.1806   0.0914      0.1810
>       43     44   33.7    0.1230   0.0828      0.1229
> Segmentation fault
>
> Since this particular revision did not change mdp settings, I presume
> MDP files from Justin's tutorial are fine.
>
> Regards,
> Vedran
>
> [1]
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
> [2]
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp
>
> --
> Vedran Miletić
> vedran.miletic.net
> --
> Gromacs Developers mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers
> or send a mail to gmx-developers-request at gromacs.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20170515/22ba36a4/attachment.html>