That's true, a lot of redundant stuff there and once again these are very basic forcefield facts for what biochem folks do. In my case, I have a bunch of very simple situations in crystal structures, but now I gotta use CHARMM or AMBER (lipids!) and charge assignment (half the time perfectly applicable to organic chemistry, yet entirely untouched in this field) in those simple situations becomes a challenge, especially when they control critical physics in the system. All in all, I hate reading detailed FF documentation. However, so as not to post questions like a good 90% of what we see on this board, I'm pretty sure I'll have to with CHARMM. I will do my best not to contribute to the whole "please do my job for me" effort here. :) As I told Mark, it is the developers' fault -- people use the incorrect tool just because it is a great piece of software. Take it as a compliment.
As always, thanks. Alex On Wed, Aug 2, 2017 at 12:59 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 8/2/17 2:52 PM, Alex wrote: > >> Yeah, those are indeed there for the particular molecules, thanks. I >> understand that this is the only way to go, it's just that my use of GMX >> is >> somewhat different in that I rarely use molecules in the normal sense, and >> OPLS-AA, being a LEGO for simple groups, has been very convenient with >> that >> catalog you mentioned. Like, place a carboxyl termination somewhere, or >> have a hole in a bulk sheet of graphene, etc. >> >> > All additive force fields are constructed in the same way, from building > blocks. It's just that OPLS-AA uses a huge amount of (redundant in many > cases) atom types and can be mapped to different charges based on different > situations. It's also why OPLS-AA has separate bonded and nonbonded atom > types. There is greater diversity among nonbonded types but fewer bonded > types, reducing the dimensionality of the internal parameters rather than > having huge amounts of duplicated bonded parameters for types that really > aren't different. > > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- 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.
