-
2
-
-
0037156101
-
-
Laio, A.; VandeVondele, J.; Röthlisberger, U. J. Chem. Phys. 2002, 116, 6941.
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 6941
-
-
Laio, A.1
VandeVondele, J.2
Röthlisberger, U.3
-
6
-
-
15444370709
-
Time-dependent density functional theory
-
Fiolhais, C., Nogueira, F., Marques, M. A. L., Eds.; Springer-Verlag: Berlin
-
Marques, M. A. L.; Gross, E. K. U. Time-Dependent Density Functional Theory. In A Primer in Density Functional Theory; Fiolhais, C., Nogueira, F., Marques, M. A. L., Eds.; Springer-Verlag: Berlin, 2003; Vol.620, pp 144-184.
-
(2003)
A Primer in Density Functional Theory
, vol.620
, pp. 144-184
-
-
Marques, M.A.L.1
Gross, E.K.U.2
-
7
-
-
0242408307
-
-
Sulpizi, M.; Carloni, P.; Hutter, J.; Röthlisberger, U. Phys. Chem. Chem. Phys. 2003, 5, 4798.
-
(2003)
Phys. Chem. Chem. Phys.
, vol.5
, pp. 4798
-
-
Sulpizi, M.1
Carloni, P.2
Hutter, J.3
Röthlisberger, U.4
-
8
-
-
13844271384
-
-
Sulpizi, M.; Röhrig, U. F.; Hutter, J.; Röthlisberger, U. Int. J. Quantum Chem. 2004, 101, 671.
-
(2004)
Int. J. Quantum Chem.
, vol.101
, pp. 671
-
-
Sulpizi, M.1
Röhrig, U.F.2
Hutter, J.3
Röthlisberger, U.4
-
9
-
-
24344472624
-
-
Moret, M.-E.; Tapavicza, E.; Guidoni, L.; Röhrig, U. F.; Sulpizi, M.; Tavernelli, I.; Röthlisberger, U. CHIMIA Int. J. Chem. 2005, 59, 493-498.
-
(2005)
CHIMIA Int. J. Chem.
, vol.59
, pp. 493-498
-
-
Moret, M.-E.1
Tapavicza, E.2
Guidoni, L.3
Röhrig, U.F.4
Sulpizi, M.5
Tavernelli, I.6
Röthlisberger, U.7
-
10
-
-
34249930039
-
-
Frutos, L. M.; Andruniów, T.; Santoro, F.; Ferré, N.; Olivucci, M. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 7764.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 7764
-
-
Frutos, L.M.1
Andruniów, T.2
Santoro, F.3
Ferré, N.4
Olivucci, M.5
-
12
-
-
0036057017
-
-
Onida, G.; Reining, L.; Rubio, A. Rev. Mod. Phys. 2002, 74, 601.
-
(2002)
Rev. Mod. Phys.
, vol.74
, pp. 601
-
-
Onida, G.1
Reining, L.2
Rubio, A.3
-
13
-
-
67849134485
-
-
42 used in this work, uses the Tamm-Dancoff approximation
-
42 used in this work, uses the Tamm-Dancoff approximation.
-
-
-
-
15
-
-
33947704666
-
-
and references therein
-
Botti, S.; Shindlmayr, A.; Del Sole, R.; Reining, L. Rep. Prog. Phys. 2007, 70, 357, and references therein.
-
(2007)
Rep. Prog. Phys.
, vol.70
, pp. 357
-
-
Botti, S.1
Shindlmayr, A.2
Del Sole, R.3
Reining, L.4
-
17
-
-
33749353769
-
-
and references therein
-
Garbuio, V.; Cascella, M.; Reining, L.; Del Sole, R.; Pulci, O. Phys. Rev. Lett. 2006, 97, 137402, and references therein.
-
(2006)
Phys. Rev. Lett.
, vol.97
, pp. 137402
-
-
Garbuio, V.1
Cascella, M.2
Reining, L.3
Del Sole, R.4
Pulci, O.5
-
21
-
-
34147185256
-
-
Peraro, M. D.; Ruggerone, P.; Raugei, S.; Gervasio, F. L.; Carloni, P. Curr. Opin. Struct. Biol. 2007, 17, 149.
-
(2007)
Curr. Opin. Struct. Biol.
, vol.17
, pp. 149
-
-
Peraro, M.D.1
Ruggerone, P.2
Raugei, S.3
Gervasio, F.L.4
Carloni, P.5
-
22
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
23
-
-
0029633186
-
-
Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E.; Debolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys. Commun. 1995, 91, 1.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
27
-
-
0032070791
-
-
Albrecht, S.; Reining, L.; Del Sole, R.; Onida, G. Phys. Rev.. Lett. 1998, 80, 4510.
-
(1998)
Phys. Rev. Lett.
, vol.80
, pp. 4510
-
-
Albrecht, S.1
Reining, L.2
Del Sole, R.3
Onida, G.4
-
28
-
-
67849129878
-
-
44 The electrostatic interaction of the classical part with periodic boundary conditions is treated by the particle-particle, particle-mesh method: we checked that the size of the box was large enough to prevent the solute from interacting with its images, estimating such interaction energy in the presence of the water and comparing it with the thermal energy fluctuation.
-
45 70 Ry energy cutoff (indole's N-H group forms H-bonds with water), and 0.1 fs time step for the dynamics. A Nose-Hoover thermostat is applied throughout all simulations to keep the temperature constant
-
-
-
-
29
-
-
67849115432
-
-
All TDDFT calculations are obtained within the Tamm-Dancoff approximation as implemented in the CPMD 3.11.1 package. For the exchange-correlation kernel, we tested different functionals (LDA, BLYP, BP, PBE), the choice being limited by the use of a plane-wave basis set. On the other hand, plane-wave-based calculations have some advantages when performing molecular dynamics (summarized in ref 46), particularly the ability to efficiently calculate the forces on atoms that are most important in our QM/MM scheme. The same corrected Troullier-Martins pseudopotentials and elec-trostatic treatment of the classical part as for the dynamics have been used
-
All TDDFT calculations are obtained within the Tamm-Dancoff approximation as implemented in the CPMD 3.11.1 package. For the exchange-correlation kernel, we tested different functionals (LDA, BLYP, BP, PBE), the choice being limited by the use of a plane-wave basis set. On the other hand, plane-wave-based calculations have some advantages when performing molecular dynamics (summarized in ref 46), particularly the ability to efficiently calculate the forces on atoms that are most important in our QM/MM scheme. The same corrected Troullier-Martins pseudopotentials and elec-trostatic treatment of the classical part as for the dynamics have been used.
-
-
-
-
30
-
-
67849093574
-
-
GW calculations have been done by using 12 077 plane-waves and 500 electronic bands. Following ref 47, we used periodic boundary conditions and a cutoff in real space for the Coulomb potential to prevent that periodic images interact with each other. The screening function is calculated within a plasmon pole approximation. For MBPT calculations, we used codes developed within the ETSF
-
GW calculations have been done by using 12 077 plane-waves and 500 electronic bands. Following ref 47, we used periodic boundary conditions and a cutoff in real space for the Coulomb potential to prevent that periodic images interact with each other. The screening function is calculated within a plasmon pole approximation. For MBPT calculations, we used codes developed within the ETSF (www.etsf.eu/resources/software/codes).
-
-
-
-
31
-
-
67849084257
-
-
47
-
47
-
-
-
-
33
-
-
29544448844
-
-
Rogers, D. M.; Besley, N. A.; O'Shea, P.; Hirst, J. D. J. Phys. Chem. B 2005, 109 (48), 23061.
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.48
, pp. 23061
-
-
Rogers, D.M.1
Besley, N.A.2
O'Shea, P.3
Hirst, J.D.4
-
34
-
-
34247590177
-
-
Sun, M.; Ding, Y.; Cui, G.; Liu, Y. J. Phys. Chem. A 2007, 111, 2946.
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 2946
-
-
Sun, M.1
Ding, Y.2
Cui, G.3
Liu, Y.4
-
35
-
-
67849134484
-
-
-1 and the isotropic position scaling algorithm to regulate pressure as implemented in the Amber package to sample in a NPT ensemble. Electrostatic interactions were evaluated using the particle mesh Ewald method, with a cutoff for the real part of 12 Å. The same value was used for the cutoff of the van der Waals interactions
-
-1 and the isotropic position scaling algorithm to regulate pressure as implemented in the Amber package to sample in a NPT ensemble. Electrostatic interactions were evaluated using the particle mesh Ewald method, with a cutoff for the real part of 12 Å. The same value was used for the cutoff of the van der Waals interactions.
-
-
-
-
36
-
-
0001085206
-
-
Simonson, T.; Wong, C. F.; Brünger, A. T. J. Phys. Chem. A 1997, 101 (10), 1935.
-
(1997)
J. Phys. Chem. A
, vol.101
, Issue.10
, pp. 1935
-
-
Simonson, T.1
Wong, C.F.2
Brünger, A.T.3
-
38
-
-
0345276570
-
-
Röhrig, U. F.; Frank, I.; Hutter, J.; Laio, A.; VandeVondele, J.; Röthlisberger, U. Chem Phys Chem 2003, 4, 1177.
-
(2003)
Chem Phys Chem
, vol.4
, pp. 1177
-
-
Röhrig, U.F.1
Frank, I.2
Hutter, J.3
Laio, A.4
VandeVondele, J.5
Röthlisberger, U.6
-
39
-
-
0037060307
-
-
Reining, L.; Olevano, V.; Rubio, A.; Onida, G. Phys. Rev.. Lett. 2002, 88, 066404.
-
(2002)
Phys. Rev. Lett.
, vol.88
, pp. 066404
-
-
Reining, L.1
Olevano, V.2
Rubio, A.3
Onida, G.4
-
40
-
-
0037159069
-
-
Cai, Z.-L.; Sendt, K.; Reimers, J. R. J. Chem. Phys. 2002, 117, 5543.
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 5543
-
-
Cai, Z.-L.1
Sendt, K.2
Reimers, J.R.3
-
42
-
-
0004133266
-
-
Hutter, J.; Alavi, A.; Deutsch, T.; Ballone, P.; Bernasconi, M.; Focher, P.; Goedecker, S.; Tuckerman, M.; Parrinello, M. CPMD 3.11.1; Copyright IBM Corp, 1990-2006; Copyright MPI für Festkörperforschung, Stuttgart, 1997-2001, 2006.
-
(2006)
CPMD 3.11.1
-
-
Hutter, J.1
Alavi, A.2
Deutsch, T.3
Ballone, P.4
Bernasconi, M.5
Focher, P.6
Goedecker, S.7
Tuckerman, M.8
Parrinello, M.9
-
43
-
-
0002997010
-
-
Luty, B. A.; Davis, M. E.; Tironi, I. G.; van Gunsteren, W. F. Mol. Simul. 1994, 14, 11.
-
(1994)
Mol. Simul.
, vol.14
, pp. 11
-
-
Luty, B.A.1
Davis, M.E.2
Tironi, I.G.3
Van Gunsteren, W.F.4
-
45
-
-
19644400832
-
-
Von Lilienfeld, O. A.; Tavernelli, I.; Röthlisberger, U.; Sebastiani, D. Phys. Rev. Lett. 2004, 93, 153004.
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 153004
-
-
Von Lilienfeld, O.A.1
Tavernelli, I.2
Röthlisberger, U.3
Sebastiani, D.4
-
46
-
-
0000323669
-
Ab initio molecular dynamics: Theory and implementation
-
Grotendorst, J., Ed.; John Von Neumann Institute for Computing: Juelich
-
Marx, D.; Hutter, J. Ab initio molecular dynamics: Theory and Implementation. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Ed.; John Von Neumann Institute for Computing: Juelich, 2000; Vol.1, pp 301-449.
-
(2000)
Modern Methods and Algorithms of Quantum Chemistry
, vol.1
, pp. 301-449
-
-
Marx, D.1
Hutter, J.2
-
47
-
-
0000101589
-
-
Onida, G.; Reining, L.; Godby, R. W.; Del Sole, R.; Andreoni, W. Phys. Rev. Lett. 1995, 75, 818-821.
-
(1995)
Phys. Rev. Lett.
, vol.75
, pp. 818-821
-
-
Onida, G.1
Reining, L.2
Godby, R.W.3
Del Sole, R.4
Andreoni, W.5
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