I am facing a problem when calculating the lipid deuterium order
parameters for the unsaturated carbons of the sn-2 tail of POPC using
g_order with GROMACS version 4.5.4 (although I have tried other older
versions too but they all give the same results).
Firstly, I should say the the calculation of the order parameters for
the saturated sn-1 chain (and also both chains of DPPC) behave as I
would expect, and produce order parameters that compare well to
previously published simulations and experimental values.
To calculate the order parameters of the unsaturated chain I am
following the approach as given on the GROMACS website
splitting the calculation into two parts for the saturated and
unsaturated regions of the chain. The problem I am facing is that the
order parameter for carbon 9 (so the first carbon in the double bond),
calculated using the -unsat option, is much larger than expected. By
this I mean that for the two different force fields I have tested
(namely the CHARMM36 parameters of Klauda et al., and the GROMOS 53A6L
parameters of Poger et al.) the order parameter for this carbon is much
larger than the published simulation values and also much larger than
experimental values. To highlight this, I have just put the numbers I
have obtained using g_order for this carbon below, and compared to some
rough values I have estimated from figures provided in the Klauda and
Klauda estimate: 0.06
Poger estimate: 0.07
Myself and a colleague have tried looking into the code to determine how
the order parameters are calculated using the -unsat option, however we
couldn't quite follow the calculation. Hopefully someone who knows
something more about g_order can help with this problem. Again I should
stress that it appears that the main difference in order parameters
between what I have calculated and the published ones is just in this
one carbon, for both force fields. A similar issue to this has also been
reported previously on the list for this carbon of POPC using the
'Berger' force field
Thank you for any help anyone can give
Dr Thomas Piggot
University of Southampton, UK.
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