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