[gmx-users] Order parameter for double bonded lipids

[Thomas Piggot]

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
>>>>
>>>> * Please search the archive at http://www.gromacs.org/Support
>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>>
>> --
>> Dr Thomas Piggot
>> Visiting Fellow
>> University of Southampton, UK.
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

-- 
Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.