[gmx-users] Lipid parameters for GROMOS96 force fields

[Justin A. Lemkul]

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.

> 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
> 

-- 
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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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