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

[Justin A. Lemkul]

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.

Perhaps.  Diagnosing the original system that creates a problem is probably more 
useful.

> 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 

Searching "range checking error" returns 270 results on the Search page.

> 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 issue usually results from a system "blowing up":

http://wiki.gromacs.org/index.php/blowing_up

-Justin

> Inon.
> 
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
> 
>  >
>  > 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
>  >
>  > ========================================
>  >
> 
> --
> Inon   Sharony
> ינון     שרוני
> +972(3)6407634
> atto.TAU.ac.IL/~inonshar
> Please consider your environmental responsibility before printing this 
> e-mail.
> 
> 
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-- 
========================================

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

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