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 hydro...@home
people).
Inon.
Quoting "Justin A. Lemkul" <jalem...@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" <jalem...@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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