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
<mailto: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
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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.k...@monash.edu <mailto:itamar.k...@monash.edu>
============================================
--
Dr Thomas Piggot
University of Southampton, UK.
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