[gmx-users] Force Field for Bilayer Simulations with Cholesterol and Proteins

[David Ackerman]

Thank you very much for your response.

If possible, could you provide a link to the cholesterol you used as well
as which atom types were changed? I know that for instance atom types HO,
C6 and CR61 present in the Holtje cholesterol are not present in e.g.
ffg53a6. Would only those types need to be changed, not all of the CH2s etc?

Thank you,
David

On Mon, May 5, 2014 at 8:31 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/5/14, 12:39 AM, David Ackerman wrote:
>
>> Hello,
>>
>> I have been performing simulations of multi-component bilayers using
>> parameters described in the following paper:
>> http://www.ncbi.nlm.nih.gov/pubmed/23470157. They use the ffgmx
>> forcefield
>> with Berger lipid parameters included. They also use cholesterol from
>> Holtje et. al (
>> http://www.sciencedirect.com/science/article/pii/S000527360100270X),
>> which
>> was parameterized for the ffgmx force field.
>>
>> I noticed that unlike the KALP-15 GROMACS tutorial which suggests deleting
>> the default lipid-gromos Berger interactions, the authors kept those
>> interactions in the force field. In light of newer force fields, are these
>> older force fields wither Berger parameters still acceptable? The
>> cholesterol model seems commonly used, so I am unsure how to use
>> cholesterol with a newer force field.
>>
>
> Just to be clear, the my tutorial instructs the user to remove those
> interactions because they are force-field specific and otherwise override
> the nonbonded interactions produced by the normal combination rules.  If
> one seeks to use a Gromos96 representation of the protein + Berger lipids,
> leaving those interactions in place is totally invalid.
>
>
>
>> Furthermore, if I were to include proteins in the simulation, would I
>> still
>> be able to use the same ffgmx force field with Berger parameters
>> (including
>> lipid-gromos interactions)?
>>
>>
> I can't speak to the Holtje parameters, but I have taken other published
> Gromos87 cholesterol models and transferred them to Gromos96 (just a few
> atom types changed); the results of those simulations (original Gromos87
> vs. Gromos96) are essentially identical.  It is a very simple validation to
> do.
>
> My general advice is that people shouldn't be using ancient force fields
> with undocumented ad hoc changes, as is the case with gmx.ff; that is a
> major reason why it has been removed from Gromacs in the 5.0 series.
>  Newer, better, force fields exist, and all indications are that these
> Gromos96 parameter sets can be combined with Berger lipids with trivial
> modifications.  Of course, the larger debate exists over whether such a
> combination is the best model, but that's a different discussion :)
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>