[gmx-users] problem with equilibration of DLiPC membrane

[Shiva Emami]

Hi Catarina,

Many thanks for your quick reply. 
Yes the reason for choosing this temperature is doing evaluation as close as physiological temperature. Actually, there is not that much information about parameters set up for membranes with polyunsaturated fatty acid chains.
However I found a paper for DAPC with CHARMM forcefield using temperature of 303.15K. So, I believe that it's doable.

All the best,

Shiva


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Catarina A. Carvalheda dos Santos <c.a.c.dossantos at dundee.ac.uk>
Sent: Thursday, November 12, 2015 11:03 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] problem with equilibration of DLiPC membrane

Hi Shiva,

The answer to that question really depends on what you want to get from the
simulation. The normal procedure with lipids is to use a temperature just
above the phase transition to ensure that the membrane is in a
liquid-crytalline-like phase. For example, for pure DPPC, for which the
phase transition temperature rounds 314 K, a temperature of 323 K ensures
that the membrane is not in the gel phase.

Of course that this is important if you want to be as close as you can from
the physiologic behaviour, so what you should or should not do is only a
consequence of what you are interested in.

The conformational behaviour of lipid molecules highly depends on the
temperature (and other factors) and maybe in your case you are just trying
to use a temperature that is too high if you want to have a "well behaved"
system. Note that you are simulating the system at 300 K, which is
approximately 80 degrees above the phase transition.

I'm assuming that there's nothing wrong with your setup, but you should
double check it anyway. Never worked with DLiPC so I cannot help you
further.

Good luck.

On 12 November 2015 at 18:26, Shiva Emami <shemami at ucdavis.edu> wrote:

> Dear Catarina,
>
> Thank you very much for your reply. Yes, I chose the temperature 217K
> based on this website. But shouldn't I equilibrate DLiPC membrane at
> application temperature like above 280K?
>
> All the best,
>
> Shiva
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Catarina
> A. Carvalheda dos Santos <c.a.c.dossantos at dundee.ac.uk>
> Sent: Thursday, November 12, 2015 1:44 AM
> To: Discussion list for GROMACS users
> Cc: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] problem with equilibration of DLiPC membrane
>
> The phase transition temperature of DLiPC is -57 degrees (around 216 K)
> according to this
> <http://avantilipids.com/index.php?option=com_content&id=1700&Itemid=419>
> table...
>
> On 11 November 2015 at 18:48, Shiva Emami <shemami at ucdavis.edu> wrote:
>
> > ________________________________
> >
> >
> > Dear all,
> >
> > I'm a new Gromacs user and I'm trying to build a lipid membrane with 450
> > DLiPC (18:2) by using 43A1-S3 forcefield.
> >
> >
> > For membrane building, first I put  a single DLiPC molecule in small box,
> > then replicated it in x-y by genconf -nbox to get 450 lipid molecules,
> then
> > got another leaflet by editconf -rotate, followed by catting and
> combining
> > two leaflets, EM, changing Z-dimension of the box,  solvation and EM.
> >
> > When I equilibrate the membrane at lower temperature like 217 K it goes
> > well. But trying equilibration at increased temperatures like 300 K, the
> > membrane shrinks too much at NPT equilibration and area per lipid
> decreases
> > to very low values.
> >
> > Can anybody help me in this case?
> >
> > Many thanks
> >
> >
> > Shiva
> > --
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> --
> Catarina A. Carvalheda
>
> PhD Student
> Computational Biology Division
> School of Life Sciences
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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--
Catarina A. Carvalheda

PhD Student
Computational Biology Division
School of Life Sciences
University of Dundee
DD1 5EH, Dundee, Scotland, UK
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