[gmx-users] Order parameter for double bonded lipids

Merril Mathew mmathe01 at mail.bbk.ac.uk
Fri Mar 10 01:10:05 CET 2017


I am using a united atom forcefield. gromos53a6. So does that mean as long
as I avoid the double bond and the subsequent carbons after the double
bond, then the calculation is correct?  I understand it does not describe
the full lipid length but can be used to assess the monolayer behaviour


On 10 Mar 2017 12:04 a.m., "Thomas Piggot" <t.piggot at soton.ac.uk> wrote:

> The order parameters calculated for all the saturated carbons will be
> correct but the gmx order program doesn't calculate the order parameters
> for the unsaturated carbons correctly (even when using the -unsat option).
> Out of interest, is this a united-atom or all-atom force field you are
> using?
> Cheers
> Tom
> On 09/03/17 23:51, Merril Mathew wrote:
>> Hi,
>> I followed turorials found on Bevanlab by Justin. I successfully
>> calculated
>> order parameter for DPPC molecules in my system following the tutorial. My
>> question is whether the same calculation can be applied for a POPG
>> molecule
>> with a double bond in the acyl chain.? can I group all the carbon upto the
>> double bond, therefore ignoring the double bond and the rest of the
>> carbons
>> in the chain to calculate order parameter? Is that a reasonable analysis
>> to
>> measure the order of POPG molecules.? Thanks.
> --
> Dr Thomas Piggot
> Visiting Fellow
> University of Southampton, UK.
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