[gmx-users] Melting temperature for the lipid bilayer

[Mohsen Ramezanpour]

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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