Re: [gmx-users] dna, lipid simulation

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 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

Re: [gmx-users] dna, lipid simulation

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

Re: [gmx-users] dna, lipid simulation

Amit Choubey 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? I wou

Re: [gmx-users] dna, lipid simulation

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 wro

[gmx-users] dna, lipid simulation

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