Well, just because I am asking about Gromacs, doesn't mean I don't know about them interactions, especially the ones as mathematically simple as those in Gromacs... Having said that, I agree that the chain flexibility is greatly affected by bonded parameter issues.
However, the particular simulation I have in mind (translocation of a near-linear ssdna chain periodic in length) is not going to be drastically affected in this case, i.e. the order of magnitude of the desired phenomena wouldn't change. There will be some effects, of course, but I will be very suprised if it's drastic. I just come from solid-state systems and wish I had experience with Gromacs that's beyond editconf-genbox-pdb2gmx-grompp. Come to think of it, you'd set up my system in about an hour. Care to collaborate? :))) Alex JL> On 3/26/15 6:10 PM, Alex wrote: >> Yeah, I agree with Justin, this is pretty half-baked. On the other hand, I >> am not after conformational changes, ds-DNA simulations, or things of that >> nature. The things I am interested in would be mostly affected by the >> partial charges and vdW parameters, and all of those seem to be from >> standard oplsaa. >> JL> Everything in force fields is interrelated, and nucleic acids are particularly JL> prone to deficiencies in bonded parameters, as the backbone dynamics are highly JL> correlated. There's a reason why nucleic acid force fields (especially in the JL> AMBER and CHARMM families) have undergone continual development for the better JL> part of 20 years. JL> See, for instance, dx.doi.org/10.1021/jz500557y JL> -Justin JL> -- JL> ================================================== JL> Justin A. Lemkul, Ph.D. JL> Ruth L. Kirschstein NRSA Postdoctoral Fellow JL> Department of Pharmaceutical Sciences JL> School of Pharmacy JL> Health Sciences Facility II, Room 629 JL> University of Maryland, Baltimore JL> 20 Penn St. JL> Baltimore, MD 21201 JL> jalem...@outerbanks.umaryland.edu | (410) 706-7441 JL> http://mackerell.umaryland.edu/~jalemkul JL> ================================================== -- Best regards, Alex mailto:nedoma...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.