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