Table 2.

Summary of all simulations performed

Simulation	dTTP/Mg2+	Starting loops conformation	Residues mutated/other changes	Running time
I	Present	From regular MD	No	120 ns
II	Absent	From regular MD	No	120 ns
III	Present	From 299 K REMD replica	No	40 ns
IV	Absent	From 299 K REMD replica	No	40 ns
V	Present	From 301 K REMD replica	No	40 ns
VI	Absent	From 301 K REMD replica	No	40 ns
VII	Present	From regular MD	Langevin damping coefficient: 10 ps−1 → 15 ps−1	40 ns
VIII	Absent	From regular MD	Langevin damping coefficient: 10 ps−1 → 15 ps−1	40 ns
IX	Present	From regular MD	CHARMM force field without CMAP	40 ns
X	Absent	From regular MD	CHARMM force field without CMAP	40 ns
XI	Present	From regular MD	Arg444 → Ala444	40 ns
XII	Present	From regular MD	Arg447 → Ala447	40 ns
XIII	Present	From regular MD	Arg448 → Ala448	40 ns
XIV	Absent	From regular MD	DNA taken from crystal binary structure of pol λ	40 ns
XV	Absent	From regular MD	Thumb shifted to open form	40 ns
XVI	Present	From regular MD	Protonation state of His329: Nδ → Nɛ	40 ns
XVII	Absent	From regular MD	Protonation state of His329: Nδ → Nɛ	40 ns