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.pig...@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.a...@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@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-requ...@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.k...@monash.edu > ============================================ > > > -- > Dr Thomas Piggot > University of Southampton, UK. > > > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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