[gmx-users] Lipid parameters for GROMOS96 force fields

Kukol, Andreas a.kukol at herts.ac.uk
Thu Jan 21 11:45:59 CET 2010


Hi,

Lipid parameters for Gromos96 53a6 are available based on the publication

Kukol, A., 2009. Lipid models for united-atom molecular dynamics simulations of proteins. J. Chem. Theor. Comput.,5(3), 615-626.

Unfortunately, I did not manage yet to upload it on the new Gromacs website. Please contact me off the list for the itp-files for DPPC, DMPC, POPC and POPG for 53a6 forcefield.

Andreas


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Justin A. Lemkul
> Sent: 21 January 2010 01:36
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Lipid parameters for GROMOS96 force fields
>
>
>
> Justin A. Lemkul wrote:
> >
> >
> > Krzysztof Mlynarczyk wrote:
> >> Hello,
> >>
> >> On Peter Tieleman's website we can find topologies for various popular
> >> lipids. However those seem to be valid for the deprecated GROMOS87
> >> force field. The g96_lipids.itp file is still unavailable. I'd like to
> >> run a simulation of 7TM protein embedded into POPC membrane. G43a2x
> >> seems to be a reasonable choice for this purpose. I still need the
> >> parameters for my lipids. I am aware that combining parameters from
> >> different force fields might lead to a disaster, that's why I want to
> >> ask you:
> >> 1. Do you know any papers where POPC membrane and G43a2 force field
> >> was used?
> >
> > I've not seen one, because it has been known for some time that early
> > Gromos96 parameter sets did not reproduce long alkyl chain properties
> > particularly well.
> >
>
> Quick amendment - modifications to 43a2 and 45a3 have been made to better
> reproduce lipid properties.  Both are available for download on the Gromacs
> site
> and you can probably track down the references, as well.
>
> Sorry, read that one wrong the first time :)
>
> -Justin
>
> >> 2. If not, is there any way to derive the proper parameters for the
> >> force field of my choice using the lipid parameters from Peter
> >> Tieleman's website or e.g. the parameters published by Andreas Kukol
> >> for G53a6?
> >>
> >
> > I don't see why you need to do such reverse engineering.  The Kukol
> > parameters for lipids under 53a6 can be directly combined with a G53a6
> > protein without any issues; I believe that was the purpose of the whole
> > new derivation :)
> >
> > As an aside, you are quite right that multiple force fields within the
> > same simulation is incorrect.  However, the Berger lipid parameters may
> > be an exception to this rule, since they are really a hybridized version
> > of OPLS-UA and Gromos87 parameters (some of which were modified anyway),
> > so they really don't belong to any one particular force field.  The
> > Berger/G87 combination is widely used, but essentially amounts to the
> > following: lipid interactions are Berger-Berger or OPLS-OPLS
> > interactions, while protein-lipid interations are Berger-G87, and
> > protein-protein interactions are G87-G87.  You can see quite quickly why
> > things become complicated!
> >
> > Based on a discussion I had with Dr. Tieleman, it seems to be reasonable
> > to use the G96 parameter set of your choice in conjunction with
> > lipid.itp (Berger lipids), although other approaches may be more
> > rigorously correct (pure G96 parameters such as those by Kukol, pure
> > OPLS recently derived by Ulmschneider, or the modifications to the
> > Berger parameters from the Tieleman group, to name a few).  If you want
> > to use a G96-lipid.itp combination, I created a tutorial that teaches
> > you how to build the system and properly prepare the topology.  It is
> > linked from the Tutorials page of the Gromacs site.
> >
> > -Justin
> >
> >> Thank you in advance,
> >> Christopher
> >>
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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