[gmx-users] Order parameter for double bonded lipids

[Merril Mathew]

many thanks Tom.

On 10 Mar 2017 1:35 a.m., "Thomas Piggot" <t.piggot at soton.ac.uk> wrote:

> So this isn't a berger based PG rather a pure GROMOS one. But yes, it also
> has problems. The double bond dihedrals don't work well and so you get
> really poor order parameters after the double bond (see
> http://pubs.acs.org/doi/abs/10.1021/ct3003157 for POPC but the same is
> true of POPG). From what I remember, this itp also has extraneous dihedrals
> in the glycerol regions plus some other issues with the bonded parameters (
> http://pubs.acs.org/doi/suppl/10.1021/jp207013v) but I cannot remember
> off the top of my head the impact they made.
>
> Up to you to decide with the density calculation.
>
> Cheers
>
> Tom
>
> On 10/03/17 00:45, Merril Mathew 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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>>>>> --
>>> Dr Thomas Piggot
>>> Visiting Fellow
>>> University of Southampton, UK.
>>>
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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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