[gmx-users] Possible bug in g_hbond with implicit solvent

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 19 17:36:56 CEST 2011

On 20/08/2011 1:26 AM, Justin A. Lemkul wrote:
> Hi All,
> I wanted to solicit some feedback on what I think may be a bug related 
> to periodicity handling and/or implicit solvent simulations.  I ran 
> some simulations of a few model peptides (some helices, hairpins, etc) 
> and I got what I believed to be very inflated results for backbone 
> hydrogen bonds.  For instance, a helical peptide with only 17 residues 
> had, on average, 23.5 hydrogen bonds within the backbone alone, which, 
> judging from the configurations, couldn't really be possible.

Does the structure file input to g_hbond have a spuriously small box?


> The simulations use infinite cutoffs and a nonperiodic unit cell.  
> g_hbond identifies 26 backbone hydrogen bonds at time zero of the 
> trajectory.  If, however, I create a .tpr file from a configuration 
> with a large box (i.e., 10-nm cube) and run g_hbond on just that 
> configuration (.gro file), I get a far more sensible result - 8 
> hydrogen bonds.
> I can't recall anyone reporting anything like this before, but it 
> seems to be that it's a fairly important issue.  Before I posted to 
> redmine, I wanted to see if anyone had encountered this, too.  The 
> version I'm using is 4.5.4; I haven't tested the latest 
> release-4-5-patches yet, but I can if that would be useful.
> -Justin

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