Rerun of MD and FF

Force fields for MD and beyond

Force Field

A force field is a set of parameters with the associated rules that together can be used to describe a situation and to simulate its future.

The main problem you will encounter while studying FF is that there are very many, radically different FF. Actually, FF are everywhere around us, and touch us every day.

FF are everywhere

AH uses FF to make us buy more than we intendThe water flow in the WaalStock market swingsFire exist usage in theatresUse of electrical power throughout the countrySecondary structure of proteinsMolecular dynamicsEtcetera

FF for MD

The force field for MD and EM holds about 5 terms. These are still the ones that were understood in the 60’s. Other terms either are poorly understood, or too hard to calculate.The present ~5 terms are optimised to also capture information related to all the terms not yet in use.

FF for MD

You better look up those five terms, and understand them deeply.All five terms in the force field are used on all atom combinations every step of the simulation. Most CPU time is spent on water interactions…In MD s=v*t, F=m*a, etc. So atoms can only fly in a straight line. Therefore the time step (time before we calculate new v) is short (1-5 fs).

Here YASARA movies

Multiple minima problem

And in a high-dimensional space this problem gets very, very much worse.

The other FF

If I throw 2 dice and 1 coin inside a small coffee cup, one could expect any asymmetry in the dices to show up much stronger (I also don’t know why, but I needed a simple example).How do we check if the dices are honest?

The other FF

How did they ever find out how the DNA code translates into protein? And how would we do it today?

How do we predict RNA binding loops?

How do we predict RNA binding loops?

1) Datasets

How do we predict RNA binding loops?

1) Datasets2) Counting

How do we predict RNA binding loops?

1) Datasets2) Counting3) ΔG

How do we predict RNA binding loops?

1) Datasets2) Counting3) ΔG4) Algorithm

How do we predict RNA binding loops?

1) Datasets2) Counting3) ΔG4) Algorithm5) Validate

And now…

FF to predict secondary structureFF to predict how ruthenium oxide binds to photographic plateFF to predict which methionines are good to click a reactive group onto?FF to predict how a ligand binds to a receptorFF to predict TM helices.