[gmx-users] Order parameter for double bonded lipids
t.piggot at soton.ac.uk
Fri Mar 10 01:18:45 CET 2017
Sort of. The saturated carbons after the double bond will be correct
too, just not C9 and C10 in the double bond (as you need different
assumptions for calculating these in united-atom system which the -unsat
option is meant to do correctly but doesn't). Additionally, there are
tools out there that will work for calculating the order parameters of
the unsaturated bond if you need it.
GROMOS 53A6 is not really a lipid force field per say but there are PG
compatible lipids (Kukol, different Berger variants, GROMOS-CKP). Which
lipid parameters are you using? Lots of them don't work well at all.
On 10/03/17 00:10, Merril Mathew wrote:
> 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
>> On 09/03/17 23:51, Merril Mathew wrote:
>>> I followed turorials found on Bevanlab by Justin. I successfully
>>> order parameter for DPPC molecules in my system following the tutorial. My
>>> question is whether the same calculation can be applied for a POPG
>>> 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
>>> in the chain to calculate order parameter? Is that a reasonable analysis
>>> measure the order of POPG molecules.? Thanks.
>> Dr Thomas Piggot
>> Visiting Fellow
>> University of Southampton, UK.
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Dr Thomas Piggot
University of Southampton, UK.
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