[gmx-users] LINCS crushes

Yuri Garmay yuri.from.spb at gmail.com
Mon Oct 31 17:43:14 CET 2011

> Try minimizing again now with all bonds constrained using the output of
> the EM that ran.  Generally, if EM crashes, your system contains some
> unresolvable clash or inappropriate geometry.  Perhaps you have now relaxed
> the bad interactions sufficiently to proceed.

I had examined structure before first minimization and if it was cause I
would have been wondered. However I have tried that advice, but this didn't
solve the problem. Minimization didn't crush, but didn't lead to any
significant atom position changes too. NPT
position restrained simulation with all bonds constrained crushes with
minimized structure, but the same with hbonds constrained doesn't. The
former produces exploded DMSO structures, the latter produces visually
correct trajectory. So, It seems that structure is not the matter.

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