Mark Abraham wrote:
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?
It does, and I suspect this is where the problem ultimately lies. For the
simulation, with "pbc = no" the box vectors get ignored and everything is fine.
For analysis, however, it seems that the PBC routines are still trying to fit
everything into that tiny box and thus basically all possible H-bonds are
detected as being present because the distances are so small.
Re-generating the .tpr file with a new, larger, box does not fix the problem,
likely because the .xtc still has the tiny box. Manipulating the trajectory
with trjconv -box -center seems to work, though. So I suppose this is an
acceptable workaround, though it still may be a problem worth looking into.
Thanks for the inspiration; hadn't thought about trying to change the box after
the fact :)
-Justin
--
========================================
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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