[gmx-users] Melting temperature for the lipid bilayer

Wed Nov 23 21:37:29 CET 2016

You started a run with a liquid state conformation and it formed a gel on its own at 350K ? Fair enough. You're using the proper charmm force switching and cutoffs?

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
Sent: 23 November 2016 15:31:53
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Melting temperature for the lipid bilayer

Hi Christopher,

I took the second approach by running simulations for 5 different
temperatures of 5 degrees intervals. (350, 355, 360, 365)
I will not pick any specific temperature as melting T. However, I can see
the shift between 355 and 365 K, representative of going to a new phase
(Liquid_disorder) in 365 K.
Visualization is also enough to see that 350 is in gel phase.

Cheers

On Wed, Nov 23, 2016 at 12:28 PM, Christopher Neale <
chris.neale at alum.utoronto.ca> wrote:

> I presume you're heating your bilayer up slowly to assess the melting
> temperature? This method will give you an estimated melting temperature
> that is equal to the true melting temperature of that Hamiltonian in
> simulation only if you go infinitely slowly. At finite heating speeds, your
> observed melting temperature will be greater than or equal to the true
> simulation melting temperature.
>
> You have to go slower than you might expect. For instance, even 0.15 K/ns
> overestimates the melting temperature (on average, of course).
>
> On the other hand, if you're evaluating the Tm by running simulations at
> various constant temperatures and you call the Tm the temperature at which
> you see 50% gel and 50% liquid dynamically interconverting many times then
> your estimate should be correct for the Hamiltonian you selected (though I
> expect this approach to be way beyond current computational abilities).
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mohsen
> Ramezanpour <ramezanpour.mohsen at gmail.com>
> Sent: 22 November 2016 16:40:08
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Melting temperature for the lipid bilayer
>
> 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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> >
> >
> > --
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> >
>
>
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