[gmx-users] dna, lipid simulation

[Thomas Piggot]

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 
> <mailto: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
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- 
>
> -- 
>
>
> "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 <mailto:Itamar.Kass at monash.edu>
> ============================================

-- 
Dr Thomas Piggot
University of Southampton, UK.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101205/ac0d83fc/attachment.html>