issues with h-bond calculation in gromacs-4.6.6

[GoogleCodeExporter]

What steps will reproduce the problem?
just follow the steps in https://code.google.com/p/plumx/wiki/helloWorld
or https://code.google.com/p/plumx/wiki/helloWorldPep

What is the expected output? What do you see instead?
The Ala 10-mer should stay a helix but it unfolded;
The membrane-peptide simulation just crashed

What version of the product are you using? On what operating system?
gromacs 4.6.6; Fedora 18;

Please provide any additional information below.

Original issue reported on code.google.com by dejun....@gmail.com on 20 Nov 2014 at 3:46

[GoogleCodeExporter]

Wrong GMXRC file was sourced.

Original comment by tristan....@gmail.com on 20 Nov 2014 at 6:59

• Changed state: Invalid

[GoogleCodeExporter]

The membrane-peptide simulation still crashed even with the right GMXRC file

Original comment by dejun....@gmail.com on 20 Nov 2014 at 8:30

[GoogleCodeExporter]

Original comment by tristan....@gmail.com on 21 Nov 2014 at 6:20

• Changed state: Started

[GoogleCodeExporter]

> Fatal error:
> A tabulated bond interaction table number 2 is out 
> of the table range: r 6.122015, between table 
> indices 3061 and 3062, table length 1501
> For more information and tips for troubleshooting, 
> please check the GROMACS

> This happened only if the patched charge-group 
> kernel was activated by setting GMX_NBLISTCG to 1 -- 
> were it not set, the simulation seemed to run fine. 
> At first I thought a simple energy minimization would 
> help but it didn't. I then took out the protein out 
> from the gro file and the corresponding charge-group 
> definitions in the ndx and mdp files, i.e., only a 72 
> POPC membrane was left, and re-ran with or without the 
> GMX_NBLISTCG set. What I found was the membrane was 
> fine without GMX_NBLISTCG set but it disintegrated  
> with GMX_NBLISTCG = 1.

I'm also seeing strange behavior with Gromacs 4.6.6. I can't reproduce your 
table error, but the simulation crashes. Gromacs 4.5.4 and 4.6.6 don't compute 
the same H-bond energies frame by frame. I'm looking into it.

Original comment by tristan....@gmail.com on 21 Nov 2014 at 8:44

• Changed state: Accepted