[gmx-users] Order parameter for double bonded lipids

Fri Mar 10 08:22:40 CET 2017

Is the modified parameter file for POPG from your work available online?

Merril.

On 10 Mar 2017 7:05 a.m., "Merril Mathew" <mmathe01 at mail.bbk.ac.uk> wrote:

> 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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>