[gmx-users] CHARMM36 for GMX

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================