[gmx-users] System almost blowing up

Dayhoff, Guy gdayhoff at health.usf.edu
Mon Apr 3 19:42:49 CEST 2017


   I’m receiving a couple (~15) EM did not converge warnings as well as a few (~3) 1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but recovers. Is this “recovery” 
system dependent? Should I take these messages (even without the subsequent crash) to indicate an
underlying issue with my system/topology or equilibration? I’m not ignoring or circumventing any warning
during pdb2gmx, or any other commands.  

For more context: I’m running the Drude-2013 forcefield, with a dt of .5fs emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting structures were minimized
in vacuum, then solvated and minimized once again prior to the posres equilibration. 

My Best,
    Guy Dayhoff


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