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.

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.


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