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 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 listgmx-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 -- gmx-users mailing listgmx-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
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 would suspect that the CHARMM force fields could cover this quite nicely. There is no tutorial for exactly what you want, but in principal, is very similar to the membrane protein tutorial I wrote (see http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations), although if you choose to use CHARMM, there is no need to mess with topologies; everything you need should be built in. The same fundamentals apply, though. -Justin Any help will be really appreciated. Thank you amit -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
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 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 -- gmx-users mailing list gmx-users@gromacs.org mailto: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 mailto: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 mailto:itamar.k...@monash.edu -- Dr Thomas Piggot University of Southampton, UK. -- gmx-users mailing listgmx-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
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 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 listgmx-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 listgmx-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 -- gmx-users mailing listgmx-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
[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. Thank you amit -- gmx-users mailing listgmx-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
