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.
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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