So I’ve entered the realm of molecular dynamics and I am constantly hearing this term “Force Fields”. The term has felt so loose and not really quantifiable perhaps dawning on magic…there is something going on under the hood that I think can only really be discovered by looking at the raw data.
Here’s a result of that….
Since I joined the University of Maryland (UM) cohort figured I would check out what the folk in this new city have on the block.
CHARMM is one of these force fields that hangs in the molecular dynamics space and stems from my new phd gig, so…what exactly are these files?
Click 1: CHARMM Additive Force Field Files
Click 2: July 2020 update (might as well get the most recent)
Quick unzip…..
What are these prm files? Lets find out..
Click 3: par_all22_prot.prm
Alright, starting off at the intro docs seems…nothing too crazy
Scrolling through and 86 lines inlook at this, rows and rows of data with a reference to some numbers. And that’s our meat..something quantifiable about these force fields.
And this is what these force fields are…. looking at the equation below what do you think this is?
I didn’t get it either at first, this is Hooke's law! Remember from way back in chemistry perceiving chemical bonds as springs etc or perhaps high school physics. Well, what they’ve done and this is why it’s so famous, they’ve covered an extensive and exhaustive list of different atoms in different scenarios and taken the measurements of Hooke's law.
So when folk is deciding parameters or force fields, they are looking at which force field best works for their particular system based on these numbers. There’s probably a lot more under the hood that’s going on but finally starting to grasp this concept.
Big ups to Paween (Post Doc) for answering my relentless questions and helping me understand molecular dynamics….
