[gmx-users] Melting temperature for the lipid bilayer

[Mohsen Ramezanpour]

It is worth mentioning that with Gromos53a7, the model was made by merging
head group and tails, I got T= 353 K for the right phase.

On Tue, Nov 22, 2016 at 2:37 PM, Mohsen Ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> Hi Justin,
>
> Comments interspersed.
>
> On Tue, Nov 22, 2016 at 1:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 11/21/16 3:28 PM, Mohsen Ramezanpour wrote:
>>
>>> Dear gromacs users,
>>>
>>> Running simulation on a lipid bilayer made by Charmm-GUI, there is about
>>> 24
>>> degrees difference between the reported temperature in Avanti and what I
>>> see in my simulations for getting a liquid disordered (L_disorder)
>>> bilayer.
>>>
>>>
>> How are you quantifying the transition in the simulation?
>
> Mainly by diffusion constant and diffusion graph. However, diffusion
> constant, bilayer thickness and area per lipid all have a shift.
> Order parameters are also higher for lower temperatures.
>
>>
>>
>> I am using all-atom Charmm36 FF for simulations.
>>>
>>
>> What is the lipid?
>>
> DSPS
>
>>
>> I know that it is not possible to get an exact match between experimental
>>> and simulation T values for L_alpha phase of bilayers, but I am not sure
>>> if
>>> these gap seems reasonable or there is something wrong in my
>>> simulations. I
>>> have checked the bonds in tails and apparently, everything looks fine
>>> with
>>> topology.
>>>
>>>
>> A gap of 24 degrees is quite substantial.  I would not consider that
>> outcome to be sufficiently accurate.
>>
>
> The melting temperature for DSPS is 68 centigrade (341 K). The
> liquid_disordered one is about 365 K (at least one with reasonable
> characteristics of liquid_disorder phase).
>
>>
>> However, based on this, doing simulation in L_alpha phase requires hight T
>>> values (close to 85 or 90 degrees of centigrade) which makes me worry
>>> about
>>> the water molecules in the system. It is a high temperature for water
>>> molecules.
>>>
>>>
>> Agreed, but TIP3P has a ton of other problems, so this is probably the
>> least of our concerns at the moment.
>>
>
>> -Justin
>>
>> Its worth mentioning that bilayer structural properties like lipid order
>>> parameters match available experimental data for these high T values.
>>>
>>> Please let me know your opinion.
>>>
>>> Cheers
>>> Mohsen
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>
>
>
> --
> *Rewards work better than punishment ...*
>



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