[gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

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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