[gmx-users] Re: Re: Unexplained crashes with Gromacs-4.0 & Neighbor Searching

Mark Abraham 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 
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



More information about the gromacs.org_gmx-users mailing list