[gmx-users] CHARMM36 for GMX

Alex nedomacho at gmail.com
Wed Aug 2 21:50:31 CEST 2017

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

As always, thanks.


On Wed, Aug 2, 2017 at 12:59 PM, Justin Lemkul <jalemkul at 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
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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