chris.ne...@utoronto.ca wrote:
Dear Thomas:
I agree with your conclusions about g_order.
My usage of the Berger POPC lipids in combination with the g_order
command (as per the instructions in
http://www.gromacs.org/Documentation/Gromacs_Utilities/g_order ) yields
order parameters of 0.193 and 0.051 for the first and second
carbons in the double bond at 300K. This is similar to but, as expected,
slightly larger than the values described in
http://www.sciencedirect.com/science/article/pii/S0014579305014365 where
they simulated at 310K and also used g_order. I suspect that one could
find tens of publications that use g_order and have published similar
values. The Poger paper (On the Validation of Molecular Dynamics
Simulations of Saturated and cis-Monounsaturated Phosphatidylcholine
Lipid Bilayers: A Comparison with Experiment) gives clearly different
values for the first carbon in the double bond than is reported by
g_order. One probable reason that this has gone unnoticed so long is
that there appears to be no experimental oleoyl order parameters -- as
far as I know -- if somebody finds them, please post them.
Cited in Klauda:
dx.doi.org/10.1021/bi00338a027
I also found:
dx.doi.org/10.1007/s00249-005-0482-z
-Justin
I took a look at the source and it is clearly incorrect for the i+1
unsaturated partner in a double bond over i->i+1. I have developed a new
version of g_order to fix this, but I'd like to test it first. If we
could agree on a single .xtc file to analyze and compare our values then
that would be great. I can provide you with one of mine (Berger lipids)
or you can provide me with one of yours (off-list).
Thanks,
Chris.
--
========================================
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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