Appendix 1—table 1.

Simulation details.

DOI: http://dx.doi.org/10.7554/eLife.17505.036

Method	label	system	init	length	force field	CVs	parameters	T (K)	software version
PathMetaD	RUN1	L99A	G	667 ns	CHARMM22*	$S_{path}$,$Z_{path}$	$\gamma$=20†, ${\tau }_D$=1 ps‡,${\tau }_G$=1 ps§, ${\omega }_0$=1.5¶	298	PLUMED2.1, GMX4.6
PathMetaD	RUN2	L99A, G113A, R119P	G	961 ns	CHARMM22*	$S_{path}$,$Z_{path}$	$\gamma$=20, ${\tau }_D$=1 ps, ${\tau }_G$=1ps, ${\omega }_0$=1.5	298	PLUMED2.1, GMX5.0
CS-restrained MD	RUN3	L99A	E	252 ns	CHARMM22*		N#=4, ${ϵ}_{CS}=24$**	298	PLUMED2.1, ALMOST2.1, GMX5
CS-restrained MD	RUN4	L99A	E	233 ns	CHARMM22*		N=2, ${ϵ}_{CS}=24$	298	PLUMED2.1, ALMOST2.1, GMX5
CS-restrained MD	RUN5	L99A	E	221 ns	CHARMM22*		N=2, ${ϵ}_{CS}=12$	298	PLUMED2.1, ALMOST2.1, GMX5
CS-restrained MD	RUN6	L99A	E	125 ns	AMBER99sb*ILDN		N=4, ${ϵ}_{CS}=24$	298	PLUMED2.1, ALMOST2.1, GMX5
CS-restrained MD	RUN7	L99A	E	190 ns	AMBER99sb*ILDN		N=2, ${ϵ}_{CS}=12$	298	PLUMED2.1, ALMOST2.1, GMX5
CS-restrained MD	RUN8	L99A, G113A, R119P	G	204 ns	CHARMM22*		N=4, ${ϵ}_{CS}=24$	298	PLUMED2.1, ALMOST2.1, GMX5
CS-restrained MD	RUN9	L99A, G113A, R119P	G	200 ns	CHARMM22*		N=2, ${ϵ}_{CS}=24$	298	PLUMED2.1, ALMOST2.1, GMX5
Reconnaissance MetaD	RUN10	L99A	G	120 ns	CHARMM22*	2,3,4,5	$\mathrm{\Delta }T$=10000††, $\mathrm{\Delta }t$=250	298	PLUMED1.3, GMX4.5
Reconnaissance MetaD	RUN11	L99A	G	85 ns	CHARMM22*	2,3,4,5	10000, 250	298	PLUMED1.3, GMX4.5
Reconnaissance MetaD	RUN12	L99A	G	41 ns	CHARMM22*	2,3,4,5,7,8	100000, 500	298	PLUMED1.3, GMX4.5
PT-WT-MetaD	RUN13	L99A	G	961 ns	CHARMM22*	1,2,3,7,8	$\gamma$=20, ${\omega }_0$=0.5	297 298‡‡ 303 308 316 325 341 350 362	PLUMED 1.3, GMX4.5
PT-WT-MetaD	RUN14	L99A	G	404 ns	CHARMM22*	1,2,3,6,7	$\gamma$=20, ${\omega }_0$=0.5	297 298 303 308 316 325 333 341 350	PLUMED 1.3, GMX4.5
PT-WT-MetaD	RUN15	L99A	G	201 ns	CHARMM22*	1,2,3,6	$\gamma$=20, ${\omega }_0$=0.5	297 298 303 308 316 325 333 341 350	PLUMED 1.3, GMX4.5
PT-WT-MetaD	RUN16	L99A	G	511 ns	CHARMM22*	1,2,3,4,5	$\gamma$=5, ${\omega }_0$=0.5	295 298 310 325 341 358 376	PLUMED 1.3, GMX4.5
PT-WT-MetaD	RUN17	L99A	G	383 ns	CHARMM22*	1,2,3,4,5	$\gamma$=20, ${\omega }_0$=0.5	298 305 313 322 332 337 343	PLUMED 1.3, GMX4.5
PT-WT-MetaD	RUN18	L99A	E	365 ns	CHARMM22*	1	$\gamma$=20, ${\omega }_0$=0.5	298 302 306 311 317 323 330 338	PLUMED 1.3, GMX4.5
plain MD	RUN19	L99A	G	400 ns	CHARMM22*			298	GMX5.0
plain MD	RUN20	L99A	E	400 ns	CHARMM22*			298	GMX5.0
plain MD	RUN21	L99A	G	400 ns	AMBER99sb*ILDN			298	GMX5.0
plain MD	RUN22	L99A	E	400 ns	AMBER99sb*ILDN			298	GMX5.0
plain MD	RUN23	L99A,G113A,R119P	G	400 ns	CHARMM22*			298	GMX5.0
plain MD	RUN24	L99A,G113A,R119P	E	400 ns	CHARMM22*			298	GMX5.0
plain MD	RUN25	L99A,G113A,R119P	G	400 ns	AMBER99sb*ILDN			298	GMX5.0
plain MD	RUN26	L99A,G113A,R119P	E	400 ns	AMBER99sb*ILDN			298	GMX5.0
InMetaD	RUN27-68§§	L99A	G		CHARMM22*	$S_{path}$,$Z_{path}$	$\gamma$=20, ${\tau }_G$=80 ps, ${\omega }_0$=1.0, ${\sigma }_S$=0.016¶¶, ${\sigma }_Z$=0.002##	298	PLUMED2.1, GMX5
InMetaD	RUN69-104***	L99A	E		CHARMM22*	$S_{path}$,$Z_{path}$	$\gamma$=20, ${\tau }_G$=80 ps, ${\omega }_0$=1.0, ${\sigma }_S$=0.016, ${\sigma }_Z$=0.002	298	PLUMED2.1, GMX5
InMetaD	RUN105-119	L99A,G113A,R119P	G		CHARMM22*	$S_{path}$,$Z_{path}$	$\gamma$=15, ${\tau }_G$=100ps, ${\omega }_0$=0.8, ${\sigma }_S$=0.016¶¶, ${\sigma }_Z$=0.002##	298	PLUMED2.2, GMX5.1.2
InMetaD	RUN120-134	L99A,G113A,R119P	E		CHARMM22*	$S_{path}$,$Z_{path}$	$\gamma$=15, ${\tau }_G$=100 ps, ${\omega }_0$=0.8, ${\sigma }_S$=0.016¶¶, ${\sigma }_Z$=0.002##	298	PLUMED2.2, GMX5.1.2
ABMD	RUN135-154	L99A-Benzene	bound		CHARMM22*	$RMS{D}_{benzene}$	K=50 KJ · mol−1 · nm−2, ${\displaystyle S_{target}=4.0}$ nm	298	PLUMED2.2, GMX5.1.2
ABMD	RUN155-174	L99A-Benzene	bound		CHARMM22*	$RMS{D}_{benzene}$	K=20 KJ · mol−1 · nm−2, ${\displaystyle S_{target}=4.0}$ nm	298	PLUMED2.2, GMX5.1.2

^†$\gamma$ is the bias factor.

^‡${\tau }_D$ is the characteristic decay time used for the dynamically-adapted Gaussian potential.

^§${\tau }_G$ is the deposition frequency of Gaussian potential.

^¶${\omega }_0$ is the height of the deposited Gaussian potential (in KJ · mol⁻¹).

^# N is the number of replicas.

**${ϵ}_{CS}$ is the strength of chemical shift restraints (in KJ · mol⁻¹ · ppm⁻²).

^††$\mathrm{\Delta }T$ means RUN_FREQ and $\mathrm{\Delta }t$ means STORE_FREQ. Other parameters: BASIN_TOL=0.2, EXPAND_PARAM=0.3, INITIAL_SIZE=3.0.

^‡‡ Replica at 298 K is the neutral replica without energy bias.

^§§42 trajectories collected for G-to-E transitions.

^¶¶${\sigma }_S$ is the Gaussian width of $S_{path}$.

^##${\sigma }_Z$ is the Gaussian width of $Z_{path}$ (in nm²).

***36 trajectories collected for E-to-G transitions.