[gmx-users] Gromos96 53a6 and Berger Lipids

[Piggot T.]

Hi,

Neither of the two papers you mentioned use the Berger lipid parameters, rather they both use purely GROMOS lipid force fields. This is plain GROMOS 45A3 for the Chandrasekhar et al. paper (using older, original, GROMOS DPPC lipid charges). This force field doesn't reproduce the properties of DPPC well and will rapidly enter a gel phase unless you use a surface tension or fixed box size (which is not recommended). In the case of the Kukol work, this is a modified 53A6 force field with the QM charges of Chiu et al. (the same charges used in the Berger lipids and in the vast majority of other united-atom PC lipid force fields) and a larger van der Waals radius (atom type CH0) for the carbonyl carbons (as originally suggested in another paper by Chandrasekhar et al.). With both the increase in van der Waals radius and change in charges, DPPC membranes behave fairly well when compared to experimental determined membrane properties. I would note, however, that there are issues with some of the other lipid parameters provided in the Kukol paper (POPC/POPG parameters). If you care about this, I can point you to some papers for more details. As for your question, if you wish to use these parameters you are correct that all you need to do is to include the itp files in your topology. 

If you are just simulating membranes, you don't need to worry about the combination of the Berger parameters with anything else (well, apart from water/ions, etc.). With the Berger lipids, people typically talk about combining them with protein force fields (GROMOS/OPLS/AMBER ones) when they are wanting to do membrane and protein simulations, as is the case in the tutorial (note, combining different force fields is generally not a good thing to do, but due to the mix of parameters that make up the Berger lipids it has shown to be acceptable in this case). As for whether the Berger lipid parameters reproduce the experimental properties of DPPC membranes, there are numerous publications out there on this. In general, Berger DPPC membranes behave ok but there are probably better lipid force fields available. If you move beyond phosphatidylcholine lipids, the Berger parameters don't tend to behave well for other types of phospholipids (again, there are lots of publications out there regarding this).

Hopefully this makes things a bit clearer.

Cheers

Tom

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Kindlein, Moritz [moritz.kindlein at tum.de]
Sent: 25 January 2016 14:02
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Gromos96 53a6 and Berger Lipids

Hi all,

I would appreciate your opinion on a quite often discussed topic.

I am doing simulations of triglycerides and phosphoglycerides, and I am currently using the combination of gromos96 53a6 and Berger Lipid parameters as suggested in Justin Lemkuls Tutorial.
If I am right, this combination has been shown to fail to reproduce the experimental parameters of DPPC membranes to satisfactory accuracy quite a while ago. F.e. see the following papers:
Kukol 2009:        10.1021/ct8003468
Chandrasekhar et al. 2005:         10.1080/08927020500134243

So my question are:

1.       The gromos96 53a6 and Berger Lipid combination is still used in the tutorial, so I am wondering if there are any newer validations for this combination, which I am missing? How would you decide if this is a valid combination?

2.       Is there a similar tutorial (like KALP-15) which shows how to set up the gromos96 53a6 and Kukol combination? Or do I only have to include the .itp files of the Kukol-paper (see above) in my topology?

Any answers are appreciated very much:)! I hope I didn't miss some already existing answers in the mailing list.

Best regards,
Moritz



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