[gmx-users] Re: Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching
Mark.Abraham at anu.edu.au
Thu May 28 15:45:23 CEST 2009
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 Hydrogen at home people).
This "commonly-reported problem" is treated briefly here
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.
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