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?
Mark
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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