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

[Inon Sharony]

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).

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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