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

[Justin A. Lemkul]

Your problem is unrelated to the bug.  Something in your system is crashing; 
this is a commonly-reported problem (search the archives).

Your system only contains three atoms?

-Justin

Inon Sharony wrote:
> 
> 
> (Thanks, Justin)
> 
> I'm using GMX 4.0.4 compiled in double-precision. I perform an 
> equilibrating run, which goes well (300K). Then I perform a cooling run 
> which is identical except that one of the atoms is coupled to a bath at 
> 0K, where I get the following error message:
> 
> Source code file: nsgrid.c, line: 357
> 
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 216 ]
> 
> 
> 
> In response to the suggestion within the message, my tiny three-atom 
> molecule is optimized to a force of 1E-9.
> I also turned off Dynamic Load Balancing, in the hope that this might 
> help, but alas...
> 
> Any thoughts on what I might be doing wrong, and how I could check for 
> it/them?
> 
> 
> --
> Inon   Sharony
> ינון     שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing this 
> e-mail.
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>  >
>  > Hi Inon,
>  >
>  > Berk implemented the fix for the release of version 4.0.2; it has
>  > been fixed for quite some time.
>  >
>  > The bugzilla entry is #229 if you would like to read the details of
>  > the problem and the solution.
>  >
>  > -Justin
>  >
>  > Inon Sharony wrote:
>  >>
>  >>
>  >> Hi Justin!
>  >>
>  >> Just wondering - do you know whether the problem with Range Checking
>  >> got corrected somehow?
>  >>
>  >> I checked the bugzilla but found no report of your bug.
>  >>
>  >> My system's energy minimized to a force of 1E-9, so I don't think
>  >> that's where my problem is...
>  >>
>  >> I understand that I might disable Dynamic Load Balancing to fix this
>  >> or somehow get around the Domain Decomposition (I don't know how to
>  >> do the latter). How did you deal with the problem?
>  >>
>  >> (There was also some talk about barostats, so I just want to make
>  >> sure that you know I'm not using one)
>  >>
>  >> --
>  >> Inon   Sharony
>  >> ינון     שרוני
>  >> +972(3)6407634
>  >> atto.TAU.ac.IL/~inonshar
>  >> Please consider your environmental responsibility before printing
>  >> this e-mail.
>  >>
>  >
>  > --
>  > ========================================
>  >
>  > Justin A. Lemkul
>  > Ph.D. Candidate
>  > ICTAS Doctoral Scholar
>  > Department of Biochemistry
>  > Virginia Tech
>  > Blacksburg, VA
>  > jalemkul[at]vt.edu | (540) 231-9080
>  > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
>  > ========================================
>  >
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================