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(Thanks, Justin)<br />
<br />
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:<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 molecule is optimized to a force of 1E-9.<br />
I also turned off Dynamic Load Balancing, in the hope that this might help, but alas...<br />
<br />
Any thoughts on what I might be doing wrong, and how I could check 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 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 href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br />
><br />
> ========================================<br />
><br />
<br />
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