id	sid	tid	token	lemma	pos
4q77fq99533	1	1	in	in	ADP
4q77fq99533	1	2	post	post	ADJ
4q77fq99533	1	3	-	-	ADJ
4q77fq99533	1	4	genomic	genomic	ADJ
4q77fq99533	1	5	computational	computational	ADJ
4q77fq99533	1	6	biology	biology	NOUN
4q77fq99533	1	7	and	and	CCONJ
4q77fq99533	1	8	bioinformatics	bioinformatic	NOUN
4q77fq99533	1	9	,	,	PUNCT
4q77fq99533	1	10	long	long	ADJ
4q77fq99533	1	11	simulations	simulation	NOUN
4q77fq99533	1	12	of	of	ADP
4q77fq99533	1	13	the	the	DET
4q77fq99533	1	14	dynamics	dynamic	NOUN
4q77fq99533	1	15	of	of	ADP
4q77fq99533	1	16	molecular	molecular	ADJ
4q77fq99533	1	17	systems	system	NOUN
4q77fq99533	1	18	,	,	PUNCT
4q77fq99533	1	19	particularly	particularly	ADV
4q77fq99533	1	20	biological	biological	ADJ
4q77fq99533	1	21	molecules	molecule	NOUN
4q77fq99533	1	22	such	such	ADJ
4q77fq99533	1	23	as	as	ADP
4q77fq99533	1	24	proteins	protein	NOUN
4q77fq99533	1	25	and	and	CCONJ
4q77fq99533	1	26	dna	dna	PROPN
4q77fq99533	1	27	,	,	PUNCT
4q77fq99533	1	28	require	require	VERB
4q77fq99533	1	29	advances	advance	NOUN
4q77fq99533	1	30	in	in	ADP
4q77fq99533	1	31	time	time	NOUN
4q77fq99533	1	32	stepping	step	VERB
4q77fq99533	1	33	computational	computational	ADJ
4q77fq99533	1	34	methods	method	NOUN
4q77fq99533	1	35	.	.	PUNCT
4q77fq99533	2	1	the	the	DET
4q77fq99533	2	2	most	most	ADV
4q77fq99533	2	3	severe	severe	ADJ
4q77fq99533	2	4	problem	problem	NOUN
4q77fq99533	2	5	of	of	ADP
4q77fq99533	2	6	these	these	DET
4q77fq99533	2	7	algorithms	algorithm	NOUN
4q77fq99533	2	8	is	be	AUX
4q77fq99533	2	9	instability	instability	NOUN
4q77fq99533	2	10	.	.	PUNCT
4q77fq99533	3	1	the	the	DET
4q77fq99533	3	2	objective	objective	NOUN
4q77fq99533	3	3	of	of	ADP
4q77fq99533	3	4	this	this	DET
4q77fq99533	3	5	dissertation	dissertation	NOUN
4q77fq99533	3	6	is	be	AUX
4q77fq99533	3	7	to	to	PART
4q77fq99533	3	8	present	present	VERB
4q77fq99533	3	9	original	original	ADJ
4q77fq99533	3	10	work	work	NOUN
4q77fq99533	3	11	in	in	ADP
4q77fq99533	3	12	constructing	construct	VERB
4q77fq99533	3	13	multiscale	multiscale	ADJ
4q77fq99533	3	14	multiple	multiple	ADJ
4q77fq99533	3	15	time	time	NOUN
4q77fq99533	3	16	stepping	stepping	NOUN
4q77fq99533	3	17	(	(	PUNCT
4q77fq99533	3	18	mts	mts	NOUN
4q77fq99533	3	19	)	)	PUNCT
4q77fq99533	3	20	algorithms	algorithm	NOUN
4q77fq99533	3	21	for	for	ADP
4q77fq99533	3	22	molecular	molecular	ADJ
4q77fq99533	3	23	dynamics	dynamic	NOUN
4q77fq99533	3	24	(	(	PUNCT
4q77fq99533	3	25	md	md	PROPN
4q77fq99533	3	26	)	)	PUNCT
4q77fq99533	3	27	that	that	PRON
4q77fq99533	3	28	allow	allow	VERB
4q77fq99533	3	29	large	large	ADJ
4q77fq99533	3	30	time	time	NOUN
4q77fq99533	3	31	steps	step	NOUN
4q77fq99533	3	32	.	.	PUNCT
4q77fq99533	4	1	first	first	ADV
4q77fq99533	4	2	,	,	PUNCT
4q77fq99533	4	3	through	through	ADP
4q77fq99533	4	4	nonlinear	nonlinear	ADJ
4q77fq99533	4	5	stability	stability	NOUN
4q77fq99533	4	6	analysis	analysis	NOUN
4q77fq99533	4	7	and	and	CCONJ
4q77fq99533	4	8	numerical	numerical	ADJ
4q77fq99533	4	9	experiments	experiment	NOUN
4q77fq99533	4	10	,	,	PUNCT
4q77fq99533	4	11	we	we	PRON
4q77fq99533	4	12	reveal	reveal	VERB
4q77fq99533	4	13	that	that	SCONJ
4q77fq99533	4	14	mts	mts	NOUN
4q77fq99533	4	15	integrators	integrator	NOUN
4q77fq99533	4	16	such	such	ADJ
4q77fq99533	4	17	as	as	ADP
4q77fq99533	4	18	impulse	impulse	NOUN
4q77fq99533	4	19	suffer	suffer	VERB
4q77fq99533	4	20	nonlinear	nonlinear	ADJ
4q77fq99533	4	21	overheating	overheating	NOUN
4q77fq99533	4	22	when	when	SCONJ
4q77fq99533	4	23	$	$	SYM
4q77fq99533	4	24	delta	delta	NOUN
4q77fq99533	4	25	t	t	PROPN
4q77fq99533	4	26	=	=	SYM
4q77fq99533	4	27	t/3	t/3	SPACE
4q77fq99533	4	28	$	$	SYM
4q77fq99533	4	29	or	or	CCONJ
4q77fq99533	4	30	possibly	possibly	ADV
4q77fq99533	4	31	$	$	SYM
4q77fq99533	4	32	delta	delta	NOUN
4q77fq99533	4	33	t	t	NOUN
4q77fq99533	4	34	=	=	NOUN
4q77fq99533	4	35	t/4	t/4	NUM
4q77fq99533	4	36	$	$	SYM
4q77fq99533	4	37	when	when	SCONJ
4q77fq99533	4	38	constant	constant	ADJ
4q77fq99533	4	39	--	--	PUNCT
4q77fq99533	4	40	energy	energy	NOUN
4q77fq99533	4	41	md	md	PROPN
4q77fq99533	4	42	simulations	simulation	NOUN
4q77fq99533	4	43	are	be	AUX
4q77fq99533	4	44	attempted	attempt	VERB
4q77fq99533	4	45	,	,	PUNCT
4q77fq99533	4	46	where	where	SCONJ
4q77fq99533	4	47	$	$	SYM
4q77fq99533	4	48	delta	delta	NOUN
4q77fq99533	4	49	t$	t$	X
4q77fq99533	4	50	is	be	AUX
4q77fq99533	4	51	the	the	DET
4q77fq99533	4	52	longest	long	ADJ
4q77fq99533	4	53	step	step	NOUN
4q77fq99533	4	54	size	size	NOUN
4q77fq99533	4	55	and	and	CCONJ
4q77fq99533	4	56	$	$	SYM
4q77fq99533	4	57	t$	t$	X
4q77fq99533	4	58	is	be	AUX
4q77fq99533	4	59	the	the	DET
4q77fq99533	4	60	shortest	short	ADJ
4q77fq99533	4	61	period	period	NOUN
4q77fq99533	4	62	of	of	ADP
4q77fq99533	4	63	the	the	DET
4q77fq99533	4	64	modes	mode	NOUN
4q77fq99533	4	65	in	in	ADP
4q77fq99533	4	66	the	the	DET
4q77fq99533	4	67	system	system	NOUN
4q77fq99533	4	68	.	.	PUNCT
4q77fq99533	5	1	second	second	ADV
4q77fq99533	5	2	,	,	PUNCT
4q77fq99533	5	3	we	we	PRON
4q77fq99533	5	4	present	present	VERB
4q77fq99533	5	5	targeted	target	VERB
4q77fq99533	5	6	molly	molly	ADV
4q77fq99533	5	7	(	(	PUNCT
4q77fq99533	5	8	tm	tm	PROPN
4q77fq99533	5	9	)	)	PUNCT
4q77fq99533	5	10	,	,	PUNCT
4q77fq99533	5	11	a	a	DET
4q77fq99533	5	12	new	new	ADJ
4q77fq99533	5	13	multiscale	multiscale	ADJ
4q77fq99533	5	14	integrator	integrator	NOUN
4q77fq99533	5	15	for	for	ADP
4q77fq99533	5	16	md	md	PROPN
4q77fq99533	5	17	simulations	simulation	NOUN
4q77fq99533	5	18	.	.	PUNCT
4q77fq99533	6	1	tm	tm	PROPN
4q77fq99533	6	2	combines	combine	VERB
4q77fq99533	6	3	an	an	DET
4q77fq99533	6	4	efficient	efficient	ADJ
4q77fq99533	6	5	implementation	implementation	NOUN
4q77fq99533	6	6	of	of	ADP
4q77fq99533	6	7	b	b	DET
4q77fq99533	6	8	-	-	PUNCT
4q77fq99533	6	9	spline	spline	NOUN
4q77fq99533	6	10	molly	molly	ADV
4q77fq99533	6	11	exploiting	exploit	VERB
4q77fq99533	6	12	analytical	analytical	ADJ
4q77fq99533	6	13	hessians	hessian	NOUN
4q77fq99533	6	14	of	of	ADP
4q77fq99533	6	15	energies	energy	NOUN
4q77fq99533	6	16	and	and	CCONJ
4q77fq99533	6	17	a	a	DET
4q77fq99533	6	18	self	self	NOUN
4q77fq99533	6	19	--	--	PUNCT
4q77fq99533	6	20	consistent	consistent	ADJ
4q77fq99533	6	21	dissipative	dissipative	ADJ
4q77fq99533	6	22	leapfrog	leapfrog	NOUN
4q77fq99533	6	23	integrator	integrator	NOUN
4q77fq99533	6	24	.	.	PUNCT
4q77fq99533	7	1	results	result	NOUN
4q77fq99533	7	2	show	show	VERB
4q77fq99533	7	3	that	that	SCONJ
4q77fq99533	7	4	tm	tm	PROPN
4q77fq99533	7	5	allows	allow	VERB
4q77fq99533	7	6	very	very	ADV
4q77fq99533	7	7	large	large	ADJ
4q77fq99533	7	8	time	time	NOUN
4q77fq99533	7	9	steps	step	NOUN
4q77fq99533	7	10	for	for	ADP
4q77fq99533	7	11	slow	slow	ADJ
4q77fq99533	7	12	forces	force	NOUN
4q77fq99533	7	13	(	(	PUNCT
4q77fq99533	7	14	and	and	CCONJ
4q77fq99533	7	15	thus	thus	ADV
4q77fq99533	7	16	multiscale	multiscale	ADJ
4q77fq99533	7	17	)	)	PUNCT
4q77fq99533	7	18	for	for	ADP
4q77fq99533	7	19	the	the	DET
4q77fq99533	7	20	numerically	numerically	ADV
4q77fq99533	7	21	challenging	challenge	VERB
4q77fq99533	7	22	flexible	flexible	ADJ
4q77fq99533	7	23	tip3p	tip3p	ADP
4q77fq99533	7	24	water	water	NOUN
4q77fq99533	7	25	systems	system	NOUN
4q77fq99533	7	26	(	(	PUNCT
4q77fq99533	7	27	jorgensen	jorgensen	PROPN
4q77fq99533	7	28	,	,	PUNCT
4q77fq99533	7	29	{	{	PUNCT
4q77fq99533	7	30	it	it	PRON
4q77fq99533	7	31	et	et	PROPN
4q77fq99533	7	32	al	al	PROPN
4q77fq99533	7	33	.	.	PUNCT
4q77fq99533	7	34	}	}	PUNCT
4q77fq99533	7	35	j.	j.	PROPN
4q77fq99533	7	36	chem	chem	PROPN
4q77fq99533	7	37	.	.	PUNCT
4q77fq99533	8	1	phys	phy	NOUN
4q77fq99533	8	2	.	.	PROPN
4q77fq99533	8	3	,	,	PUNCT
4q77fq99533	8	4	vol	vol	NOUN
4q77fq99533	8	5	79	79	NUM
4q77fq99533	8	6	,	,	PUNCT
4q77fq99533	8	7	pp	pp	PROPN
4q77fq99533	8	8	926	926	NUM
4q77fq99533	8	9	-	-	PUNCT
4q77fq99533	8	10	-935	-935	NOUN
4q77fq99533	8	11	,	,	PUNCT
4q77fq99533	8	12	1983	1983	NUM
4q77fq99533	8	13	)	)	PUNCT
4q77fq99533	8	14	while	while	SCONJ
4q77fq99533	8	15	still	still	ADV
4q77fq99533	8	16	computing	compute	VERB
4q77fq99533	8	17	the	the	DET
4q77fq99533	8	18	dynamical	dynamical	ADJ
4q77fq99533	8	19	and	and	CCONJ
4q77fq99533	8	20	structural	structural	ADJ
4q77fq99533	8	21	properties	property	NOUN
4q77fq99533	8	22	accurately	accurately	ADV
4q77fq99533	8	23	.	.	PUNCT
4q77fq99533	9	1	finally	finally	ADV
4q77fq99533	9	2	,	,	PUNCT
4q77fq99533	9	3	we	we	PRON
4q77fq99533	9	4	show	show	VERB
4q77fq99533	9	5	yet	yet	ADV
4q77fq99533	9	6	another	another	DET
4q77fq99533	9	7	new	new	ADJ
4q77fq99533	9	8	molly	molly	ADV
4q77fq99533	9	9	integrator	integrator	ADJ
4q77fq99533	9	10	,	,	PUNCT
4q77fq99533	9	11	the	the	DET
4q77fq99533	9	12	backward	backward	PROPN
4q77fq99533	9	13	euler	euler	NOUN
4q77fq99533	9	14	(	(	PUNCT
4q77fq99533	9	15	be	be	AUX
4q77fq99533	9	16	)	)	PUNCT
4q77fq99533	9	17	molly	molly	ADV
4q77fq99533	9	18	in	in	ADP
4q77fq99533	9	19	which	which	PRON
4q77fq99533	9	20	hydrogen	hydrogen	NOUN
4q77fq99533	9	21	bond	bond	NOUN
4q77fq99533	9	22	forces	force	NOUN
4q77fq99533	9	23	can	can	AUX
4q77fq99533	9	24	easily	easily	ADV
4q77fq99533	9	25	be	be	AUX
4q77fq99533	9	26	included	include	VERB
4q77fq99533	9	27	in	in	ADP
4q77fq99533	9	28	the	the	DET
4q77fq99533	9	29	averaging	averaging	NOUN
4q77fq99533	9	30	and	and	CCONJ
4q77fq99533	9	31	thus	thus	ADV
4q77fq99533	9	32	stability	stability	NOUN
4q77fq99533	9	33	might	might	AUX
4q77fq99533	9	34	be	be	AUX
4q77fq99533	9	35	further	far	ADV
4q77fq99533	9	36	improved	improve	VERB
4q77fq99533	9	37	.	.	PUNCT