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Feature #1902

Updated by Mark Abraham over 4 years ago

Topologies using complex features might accidentally place particle sites on top of each other, which can lead to strange numerical issues if they are not excluded from short-range interactions. grompp should check e.g. that no non-excluded atom pairs are at less than (say) 1% of the interaction range. That will require a neighbour search, however.

Justin's original bug report follows

Posted to gmx-developers:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2016-February/008907.html

Ligands with virtual sites randomly fail in calculations using Verlet, with or without the free energy code, as I was trying to use. The issue may not be specific to Verlet though, as the group scheme fails when the free energy code is active as well. From my original post, I have tested the following combinations:

<pre>
1. Free energy + Verlet = immediate seg fault in energy minimization
2. FE off + Verlet = seg fault
3. FE + group = seg fault
4. FE off + group = WORKS
5. Single-point energy (FE off + Verlet) = seg fault (so it is not specific to
the minimizer, as I use the md integrator in the .mdp file)
6. Generic kernels seg fault
7. Disabling SIMD (GMX_SIMD=None when running cmake) seg faults
8. Doing an absolute free energy calculation runs fine
</pre>

I have attached a .tpr file of the minimization that fails using Verlet + free energy code (i.e. the calculation that I actually want to run). It immediately seg faults for me with -nan for Coul(SR).

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