[gmx-users] dna, lipid simulation

[Amit Choubey]

Thank you all. At least now I have an idea of the starting point.

On Sun, Dec 5, 2010 at 12:31 PM, Thomas Piggot <t.piggot at soton.ac.uk> wrote:

>  I would tend to agree with Justin rather than Itamar. The GROMOS DNA
> parameters are not especially good (see
> http://www.ncbi.nlm.nih.gov/pubmed/20614923) but it depends on what you
> are wanting to look at. Another option (rather than CHARMM, which for what
> it is worth is the force field I would probably use) is you could use one of
> the AMBER forcefields for the DNA and the GAFF lipids (although I forget if
> there is DPPC available or not, I think the only fully saturated lipid
> already available might be DMPC), but keep in mind you need to use surface
> tension with these lipids. As I said the choice really depends on what you
> want to look at, so some reading of the literature and also seeing what
> other people have done for similar simulations should help.
>
> Cheers
>
> Tom
>
>
> On 05/12/10 12:42, Itamar Kass (Med) wrote:
>
> Hi Amit,
>
> The GROMOS force field had both DNA and lipids parameters, hence you can
> use it in your simulations. Moreover, there are new lipids parameters by
> David Poger and Alan Mark which I should give better results compared to the
> old set.
>
> Good luck.
>
>
> On 5 December 2010 18:09, Amit Choubey <kgp.amit at gmail.com> wrote:
>
>> Hi all,
>>
>>  This is a question unrelated to gromacs but would pose it anyway to get
>> some hints from the experts.
>> I wish to set up DNA and DPPC lipid membrane simulation. Could someone
>> please refer to a relevant forcefield/tutorial for simulation of lipids with
>> DNA?
>>
>>  Any help will be really appreciated.
>>
>>  Thank you
>> amit
>>
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>
>
>
> --
>
> --
>
>
> "In theory, there is no difference between theory and practice. But, in
> practice, there is." - Jan L.A. van de Snepscheut
>
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu
> ============================================
>
>
> --
> Dr Thomas Piggot
> University of Southampton, UK.
>
>
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