[gmx-users] problem with equilibration of DLiPC membrane

Thu Nov 12 22:34:54 CET 2015

Just to clarify, I meant that you should chose the simulation settings that
give you a physiologic-like conformational behaviour not that you should
chose a physiologic (ish) temperature regardless of the system you have in
hands.

The transition phase temperature of DAPC is around 340 K -->
http://link.springer.com/chapter/10.1007%2F978-3-319-11280-0_17

Regards,

On 12 November 2015 at 19:57, Shiva Emami <shemami at ucdavis.edu> wrote:

> 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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> > > The University of Dundee is a registered Scottish Charity, No: SC015096
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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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> Gromacs Users mailing list
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-- 
Catarina A. Carvalheda

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