CiteULike: softsimu's van der Spoel:D [10 articles]

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447.

by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl

Speeding up parallel GROMACS on high-latency networks

Journal of Computational Chemistry, Vol. 28, No. 12. (2007), pp. 2075-2084.

by Carsten Kutzner, David van der Spoel, Martin Fechner, et al.Erik Lindahl, Udo W. Schmitt, Bert L. De Groot, Helmut Grubmüller

posted to gromacs by softsimu on 2008-09-16 09:50:28 as

Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials

J. Phys. Chem. B, Vol. 105, No. 13. (5 April 2001), pp. 2618-2626.

by P. J. van Maaren, D. van der Spoel

posted to gromacs polarizability by softsimu on 2008-06-17 18:21:28 as

along with 1 person alex_bunker

The Origin of Layer Structure Artifacts in Simulations of Liquid Water

J. Chem. Theory Comput., Vol. 2, No. 1. (10 January 2006), pp. 1-11.

by D. van der Spoel, P. J. van Maaren

posted to artifacts electrostatics molecular-dynamics by softsimu on 2008-02-17 00:51:37 as

along with 2 people Scis0000002 doktornoe

Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation

J. Phys. Chem. B, Vol. 104 (2000)

by D. P. Tieleman, D. van der Spoel, H. J. C. Berendsen

posted to bibtex-import membranes micelles by softsimu on 2008-02-11 18:03:16 as

GROMACS: fast, flexible, and free.

J. Comput. Chem., Vol. 26, No. 16. (December 2005), pp. 1701-1718.

by D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, H. J. Berendsen

posted to gromacs by softsimu on 2008-01-13 22:54:07 as

along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome

A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field

The Journal of Chemical Physics, Vol. 108, No. 24. (1998), pp. 10220-10230.

by David van der Spoel, Paul J. van Maaren, Herman J. C. Berendsen

posted to force-fields reaction-field water by softsimu on 2008-01-13 22:52:39 as

along with 3 people r2s2 A_Coletta_Thesis jwagoner

Gromacs User Manual version 3.1

(2001)

by D. van der Spoel, A. R. van Buuren, E. Apol, et al.P. J. Meulenhoff, D. P. Tielemann, A. L. T. M. Sijbers, B. Hess, K. A. Feenstra, E. Lindahl, R. van Drunen, H. J. C. Berendsen

posted to gromacs by softsimu on 2007-12-12 01:33:26 as read

GROMACS 3.0: A package for molecular simulation and trajectory analysis

J. Mol. Mod., Vol. 7, No. 8. (August 2001), pp. 306-317.

by E. Lindahl, B. Hess, D. van der Spoel

posted to gromacs by softsimu on 2007-12-12 01:33:25 as read

GROMACS: A message-passing parallel molecular dynamics implementation

Comp. Phys. Comm., Vol. 91 (1995), pp. 43-56.

by H. J. C. Berendsen, D. van der Spoel, R. van Drunen

posted to bibtex-import gromacs by softsimu on 2007-12-11 21:31:03 as read

Sort by:
Order:	Default Ascending Descending
Empty fields:	Default First Last

	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to gromacs by softsimu on 2009-10-03 18:18:18 as along with 24 people and 2 groups mikaellund sunnytov parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans mmuecke sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	Speeding up parallel GROMACS on high-latency networks [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (2007), pp. 2075-2084. by Carsten Kutzner, David van der Spoel, Martin Fechner, et al.Erik Lindahl, Udo W. Schmitt, Bert L. De Groot, Helmut Grubmüller posted to gromacs by softsimu on 2008-09-16 09:50:28 as
	Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials [My Copy] J. Phys. Chem. B, Vol. 105, No. 13. (5 April 2001), pp. 2618-2626. by P. J. van Maaren, D. van der Spoel posted to gromacs polarizability by softsimu on 2008-06-17 18:21:28 as along with 1 person alex_bunker
	The Origin of Layer Structure Artifacts in Simulations of Liquid Water [My Copy] J. Chem. Theory Comput., Vol. 2, No. 1. (10 January 2006), pp. 1-11. by D. van der Spoel, P. J. van Maaren posted to artifacts electrostatics molecular-dynamics by softsimu on 2008-02-17 00:51:37 as along with 2 people Scis0000002 doktornoe
	Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation [My Copy] J. Phys. Chem. B, Vol. 104 (2000) by D. P. Tieleman, D. van der Spoel, H. J. C. Berendsen posted to bibtex-import membranes micelles by softsimu on 2008-02-11 18:03:16 as
	GROMACS: fast, flexible, and free. [My Copy] J. Comput. Chem., Vol. 26, No. 16. (December 2005), pp. 1701-1718. by D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, H. J. Berendsen posted to gromacs by softsimu on 2008-01-13 22:54:07 as along with 20 people and 2 groups arifor krapnik r2s2 janneb dsmueller oteri choonpeng sebk dimka jwm ttjoseph bilab rabio Dinler tji ashaytan robertvacha sunnytov Diego_Prada A_Coletta_Thesis Radiation_Damage Stressosome
	A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field [My Copy] The Journal of Chemical Physics, Vol. 108, No. 24. (1998), pp. 10220-10230. by David van der Spoel, Paul J. van Maaren, Herman J. C. Berendsen posted to force-fields reaction-field water by softsimu on 2008-01-13 22:52:39 as along with 3 people r2s2 A_Coletta_Thesis jwagoner
	Gromacs User Manual version 3.1 [My Copy] (2001) by D. van der Spoel, A. R. van Buuren, E. Apol, et al.P. J. Meulenhoff, D. P. Tielemann, A. L. T. M. Sijbers, B. Hess, K. A. Feenstra, E. Lindahl, R. van Drunen, H. J. C. Berendsen posted to gromacs by softsimu on 2007-12-12 01:33:26 as
	GROMACS 3.0: A package for molecular simulation and trajectory analysis [My Copy] J. Mol. Mod., Vol. 7, No. 8. (August 2001), pp. 306-317. by E. Lindahl, B. Hess, D. van der Spoel posted to gromacs by softsimu on 2007-12-12 01:33:25 as
	GROMACS: A message-passing parallel molecular dynamics implementation [My Copy] Comp. Phys. Comm., Vol. 91 (1995), pp. 43-56. by H. J. C. Berendsen, D. van der Spoel, R. van Drunen posted to bibtex-import gromacs by softsimu on 2007-12-11 21:31:03 as

softsimu's van der Spoel:D [10 articles] Export Sort

softsimu's tags

bibtex-import	3999
micelles	243
membranes	147
sds	134
dpd	114
cdw	112
actin	104
cardiolipin	95
water	85
electrostatics	78
cholesterol	76
coarse-graining	67
polymers	65
proteins	65
diffusion	58
glut	56
turing	56
salt	56
d20	52
denaturation	45
rafts	44
comt	44
ewald-summation	43
lipids	42
fusion	41
cold	41
file-import-08-10-15	39
monte-carlo	38
hemolysin	38
nopdf	38
glycolipids	37
ions	37
cell-division	36
colloids	36
vesicles	34
pressure	33
nanopores	32
alcohol	31
crumpling	31
nalp	30
dep	30
mineralization	30
glasses	29
motors	28
electrorheology	27
poisson-boltzmann	27
ethanol	26
superconductivity	26
dna	26
fission	25
peptides	25
jarzynski	25
lateral	24
folding	23
translocation	23
electrokinetics	23
asters	22
popc	22
pores	21
free-energy	21
hdl	20
overcharging	20
dmpc	20
abc	20
saponins	19
double-bond	19
peth	19
phosphatidylethanol	18
transport-pore	18
force-fields	18
nanotubes	18
molecular-dynamics	18
integrators	17
monolayers	17
instabilities	17
nmr	17
anesthesia	17
pfc	17
file-import-08-10-02	16
shear	16
dynamics	16
rotaball	16
polyelectrolytes	16
hydrophobicity	16
dppc	16
drug-delivery	15
molecular	15
cationic	15
glyco	15
mrks-diff	15
pinning	14
hydroxyapatite	14
sphingosine	14
ldl	14
anionic	14
self-assembly	14
pop	13
hydrophobicty	13
abf	13
dopc	12
copolymers	12
mitochondria	12
sirna	12
surfaces	12
binding-affinity	12
pope	12
ctab	12
free	12
friction	12
block	12
lipoproteins	11
lekner	11
sterols	11
kinesin	11
hydrodynamics	11
channels	11
clathrate	11
desmosterol	10
self-organization	10
bilayers	10
transportan	10
simulation	10
force	10
energy	10
fracture	10
gromacs	10
phase-slip	10
popg	9
amyloid	9
brownian-dynamics	9
flowers	9
wang-landau	9
surfactants	9
review	9
diffusion-proton	9
diffusion-ions	9
domains	9
melts	9
vortex	9
pressure-profile	9
detergents	8
spc	8
coulomb	8
liposomes	8
phase-field	8
viscosity	8
diffusion-protons	8
force-field	8
fields	8
charged	8
eckhaus	8
lattice-boltzmann	8
penetratin	8
dielectrophoresis	8
ftsz	8
wetting	8
ginzburg-landau	8
solvation	8
cytochrome	7
cytoskeleton	7
alzheimers	7
nacl	7
peierls	7
cytokinesis	7
thermostat	7
osteopontin	7
dendrimers	7
phase	7
microfludics	7
md	7
materials	7
mb-model	7
heparan	7
electrophoresis	6
lj-phase	6
imc	6
flux-lines	6
transitions	6
sphingomyelin	6
dmtap	6
h-bonds	6
apo-a1	6
sopc	6
nemd	6
pattern-formation	6
reptation	6
mullins-sekerka	6
vacf	6
phd-thesis	6
elasticity	6
rot	6
som	6
kosterlitz-thouless	6
granular	6
cacl	6
formation	6
peptide	6
membrane-gel	6
ion-membrane-interaction	6
photoswitches	6
s1-specificity	5
ketosterol	5
fibers	5
sph	5
neural-nets	5
commensurability	5
gels	5
supported-bilaters	5
cold-denaturation	5
stability	5
lung-surfactant	5
pme	5
electrostatics-membranes	5
nanotech	5
structure	5
stencils	5
fluid	5
pattern	5
nucleation	5
electrorotation	5
lubrication	5
methanol	5
boundary	5
rhodopsin	5
frenkel-kontorova	5
transition	5
tip4p	5
nanopumps	5
graded	5
hydrophobic	5
debye-huckel	5
pops	5
solubilization	4
systems	4
fem	4
myosin	4
flip-flop	4
electrolytes	4
magnesium	4
calcium	4
gb3	4
integrators-dpd	4
aquaporin	4
brownian-motion	4
7-dehydrocholesterol	4
peg	4
liquid-crystals	4
phase-separation	4
qs21	4
implicit-solvent	4
receptors	4
ceramides	4
heparin	4
opls	4
designability	4
scaling	4
sphingolipids	4
file-import-08-10-07	4
sialoprotein	4
micelle	4
dielectrics	4
vaccines	4
tip3p	4
spin-labels	4
charmm	4
neg-cv	4
qm-mm	4
shs	4
pi-interactions	4
polarizability	3
van-der-waals	3
dha	3
defects	3
ergosterol	3
eukaryotes	3
dewetting	3
earthquakes	3
2-4	3
soc	3
flow	3
lipoprotein	3
artifacts	3
dpc	3
sans	3
forces	3
lipid	3
phase-diagram	3
son	3
symplectic	3
endocytosis	3
ospc	3
magnetic-stripes	3
pmf	3
signaling	3
magnetic	3
dotap	3
superfluidity	3
block-copolymers	3
nanowires	3
phospholipid	3
min-oscillations	3
fokker-planck	3
amp	3
rouse	3
lipid-isomers	3
maria	3
fluids	3
henderson	3
fene	3
lanosterol	3
ferrofluids	3
amber	3
stxb	3
oil	3
namd	3
percolation	3
plotting	3
parallel-tempering	3
dppe	3
dendrites	3
molecular-simulation	3
delta	3
onions	3
mori-zwanzig	3
nose-hoover	3
lumped-mass	2
partitioning	2
protrusions	2
layer	2
guv	2
martini	2
ompf	2
fmm	2
voronoi	2
rupture	2
collapse	2
ion-channel	2
p3m	2
pna	2
caox	2
fluctuations	2
hydration	2
separation	2
self-organized-criticality	2
fluid-dynamics	2
sdw	2
instability	2
apoptosis	2
generic	2
trehalose	2
foams	2
counterion	2
critical-phenenomena	2
nanoparticles	2
dlpc	2
pe	2
lattice	2
ecoli	2
sensors	2
trotter	2
legendre	2
cholester	2
mg	2
ctabr	2
reaction-diffusion	2
dislocations	2
ab-initio	2
dft	2
gouy-chapman	2
emulsions	2
ionization	2
kpz	2
sglt	2
py	2
7dhc	2
ctac	2
multiple-time-step	2
shadow-hamiltonian	2
energies	2
stern	2
factor	2
chemical_potential	2
field	2
rna	2
laplacian	2
cyclodextrin	2
model	2
ca	2
permeation	2
polymer	2
resp	2
persistence-length	2
espresso	2
order-parameter	2
tilt	2
ostwald	2
gibbs-bogoliubov	2
magnetorheology	2
alchohol	2
toxin	2
enzymes	2
multigrid	2
crystallization	2
complex-fluids	2
dtab	2
mds	2
spinodal-decomposition	2
dendritic	2
topological	2
dspc	2
growth	2
dlvo	2
meso	2
liposome	1
pept1	1
density-functional	1
monoayers	1
transport	1
capillarity	1
troblocks	1
tension	1
phase-sl	1
osteoarthritis	1
nanocomposite	1
ligands	1
force-spectroscopy	1
fitting	1
membrane-proteins	1
prosthetic	1
glyc	1
doxorubicin	1
metallic-nanoparticles	1
tweezers	1
kohn-anomaly	1
hydrodynamocs	1
twin-range-cutoff	1
pah	1
specle	1
magnetoelectric	1
matter	1
peo	1
coatings	1
namd2	1
mscl	1
gating	1
implants	1
x-ray	1
transduction	1
stxx	1
hopping	1
lammps	1
pc	1
stokeslets	1
bacterial	1
polymer-melts	1
curvature	1
antennapedia	1
pepg	1
egf	1
cationic-lipids	1
green-kubo	1
dssp	1
dlpe	1
slab	1
invariance	1
bundles	1
barostat	1
omp	1
graphite	1
dpps	1
parameters	1
ctacl	1
saxs	1
lateral-pressure	1
kcsa	1
films	1
twin-range	1
crystals	1
aluminum	1
molecular-medicine	1
dptap	1
length	1
non-ionic	1
dope	1
dmso	1
epicholesterol	1
tutring	1
apo-b	1
cdima	1
self-gravitation	1
dmpg	1
liquid	1
madelung	1
dmpe	1
dynamical-systems	1
proylyloligopeptidase	1
pulling	1
roughening	1
of	1