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

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 19 17:26:46 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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