[gmx-users] Melting temperature for the lipid bilayer
jalemkul at vt.edu
Tue Nov 22 21:18:47 CET 2016
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?
> I am using all-atom Charmm36 FF for simulations.
What is the lipid?
> 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
A gap of 24 degrees is quite substantial. I would not consider that outcome to
be sufficiently accurate.
> 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
Agreed, but TIP3P has a ton of other problems, so this is probably the least of
our concerns at the moment.
> 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.
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
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