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

[Inon Sharony]

(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[1]
>
> ========================================
>



Links:
------
[1] http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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