Inon Sharony wrote:
I dumbed down the system (molecule) to keep the potential pitfalls to a
minimum. One of the three atoms is just a deadweight (molecular weight
9999999.9) . Could this be the problem? If so, how? I'll try simulating
a lighter molecule to see if that takes care of it.
Though this is "a commonly-reported problem", so far I failed in finding
past reference to it in the archives -- at least I can't differentiate
my problem with the one you reported, and another instance which turned
out to be because the protein topology was completely out of order (from
the hydro...@home people).
This "commonly-reported problem" is treated briefly here
http://wiki.gromacs.org/index.php/Errors#Range_Checking_error.
If you've got most of your system coupled to 300K, and a single atom
coupled to 0K, it's no surprise that your integration is unstable.
Thermostat algorithms work well in thermodynamic limits, not for
handfuls of atoms.
Mark
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