[gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

I also used the same POPG .itp and .pdb files to edit and create an
oxidised version of the molecule with aldehyde group replacing the double
bond. Is there a problem associated with parameters from A Kukol for POPG?

On 10 Mar 2017 00:45, "Merril Mathew" <mmathe01 at mail.bbk.ac.uk> wrote:

> The POPG .itp and .pdb files were obtained from,
> https://lipidbook.bioch.ox.ac.uk/package/show/id/16.html
> Author : A Kukol.
>  I used D-POPG. Should I use electron density or mass for calculating
> monolayer thickness?
>
> Merril.
>
> On 10 Mar 2017 00:36, "Thomas Piggot" <t.piggot at soton.ac.uk> wrote:
>
>> How did you get/make the itp for POPG, this isn't available from the
>> Tieleman group website. The Berger parameters don't work well for PG. For
>> example, you will see ring like structures in the head group if you look at
>> the simulations in something like VMD. The APL for bilayers (and I imagine
>> monolayers) will also be too low. You can find more details in
>> http://pubs.acs.org/doi/abs/10.1021/jp900645z (the Zhao and Elmore
>> models are Berger based ones).
>>
>> For the APL, the calculation is trivial using the box vectors (from gmx
>> energy or gmx traj). For the thickness, you can probably use gmx density to
>> create a density profile of your monolayer and work out a thickness from
>> that.
>>
>> Tom
>>
>> On 10/03/17 00:24, Merril Mathew wrote:
>>
>>> I am using Berger lipid from Dr.Tielemens website and modified the gromos
>>> forcefield to include the lipid parameters. Out of interest, Do you know
>>> any gromacs tools or other programs that calculatg the area per lipid and
>>> bilayer thickness for monolayers? I tried to use GridMAT-MD and FATSLiM
>>> but
>>> it only works with bilyer lipids. thanks.
>>>
>>> Merril.
>>>
>>> On 10 Mar 2017 00:19, "Thomas Piggot" <t.piggot at soton.ac.uk> wrote:
>>>
>>> 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.
>>>>
>>>> Cheers
>>>>
>>>> Tom
>>>>
>>>> On 10/03/17 00:10, Merril Mathew wrote:
>>>>
>>>> Hi,
>>>>>
>>>>> 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
>>>>> roughly.
>>>>>
>>>>> Merril.
>>>>>
>>>>> 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.
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
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>>>>>>
>>>>>>
>>>>>> --
>>>> Dr Thomas Piggot
>>>> Visiting Fellow
>>>> University of Southampton, UK.
>>>>
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>>>> Gromacs Users mailing list
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>>>>
>> --
>> Dr Thomas Piggot
>> Visiting Fellow
>> University of Southampton, UK.
>>
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>> Gromacs Users mailing list
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>