-
1
-
-
0036424048
-
-
Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Ann. Rev. Phys. Chem. 2002, 53, 291.
-
(2002)
Ann. Rev. Phys. Chem.
, vol.53
, pp. 291
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
2
-
-
84906402993
-
-
In this paper, we refer to the potential of mean force and reaction coordinate free energy profile interchangeably
-
In this paper, we refer to the potential of mean force and reaction coordinate free energy profile interchangeably.
-
-
-
-
5
-
-
1942455290
-
-
Kinnear, B. S.; Jarrold, M. F.; Hansmann, U. H. E. J. Mol. Graphics Modell. 2004, 22, 397.
-
(2004)
J. Mol. Graphics Modell.
, vol.22
, pp. 397
-
-
Kinnear, B.S.1
Jarrold, M.F.2
Hansmann, U.H.E.3
-
7
-
-
42149194240
-
-
Darve, E.; Rodriguez-Gomez, D.; Pohorille, A. J. Chem. Phys. 2008, 128, 144120/1.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 144120-144121
-
-
Darve, E.1
Rodriguez-Gomez, D.2
Pohorille, A.3
-
9
-
-
55949099868
-
-
Vanden-Eijnden, E.; Venturoli, M.; Ciccotti., G.; Elber, R. J. Chem. Phys. 2008, 129, 174102/1.
-
(2008)
J. Chem. Phys.
, vol.129
-
-
Vanden-Eijnden, E.1
Venturoli, M.2
Ciccotti, G.3
Elber, R.4
-
10
-
-
84986519238
-
-
Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Conmut. Chem. 1992, 13, 1011.
-
(1992)
J. Conmut. Chem.
, vol.13
, pp. 1011
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
13
-
-
0036040917
-
-
Voter, A. F.; Montalenti, F.; Germanii, T. C. Ann. Rev. Mater. Res. 2002, 32, 321.
-
(2002)
Ann. Rev. Mater. Res.
, vol.32
, pp. 321
-
-
Voter, A.F.1
Montalenti, F.2
Germanii, T.C.3
-
18
-
-
4243661501
-
-
Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Chem. Phys. Lett. 1989, 156, 472.
-
(1989)
Chem. Phys. Lett.
, vol.156
, pp. 472
-
-
Carter, E.A.1
Ciccotti, G.2
Hynes, J.T.3
Kapral, R.4
-
19
-
-
0028710015
-
-
Huber, T.; Torda, A. E.; van Gunsteren, W. F. J. Comput. -Aided Mol. Des. 1994, 8, 695.
-
(1994)
J. Comput. -Aided Mol. Des.
, vol.8
, pp. 695
-
-
Huber, T.1
Torda, A.E.2
Van Gunsteren, W.F.3
-
21
-
-
0001235532
-
-
Paci, E.; Ciccotti, G.; Ferrario, M.; Kapral, R. Chem. Phys. Lett. 1991, 176, 581.
-
(1991)
Chem. Phys. Lett.
, vol.176
, pp. 581
-
-
Paci, E.1
Ciccotti, G.2
Ferrario, M.3
Kapral, R.4
-
25
-
-
0346350789
-
-
Woods, C. J.; Essex, J. W.; King, M. A. J. Phys. Chem B 2003, 107, 13703.
-
(2003)
J. Phys. Chem B
, vol.107
, pp. 13703
-
-
Woods, C.J.1
Essex, J.W.2
King, M.A.3
-
29
-
-
84906374367
-
-
In this article, we will often refer to "phase space" constraints. Strictly speaking, the examples that we provide in this work, deal with geometrical constraints, so that "configuration space" is the more appropriate term. However, both AXD and BXD may be carried out in energy space, which involves both, coordinates and momenta, so that they are generalizable to phase space. To emphasize this generality, we often refer to phase space
-
In this article, we will often refer to "phase space" constraints. Strictly speaking, the examples that we provide in this work, deal with geometrical constraints, so that "configuration space" is the more appropriate term. However, both AXD and BXD may be carried out in energy space, which involves both, coordinates and momenta, so that they are generalizable to phase space. To emphasize this generality, we often refer to phase space.
-
-
-
-
32
-
-
34247338100
-
-
Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. J. Chem. Phys. 2007, 126, 155101/1.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101-155111
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
34
-
-
24044551638
-
-
Paci, E.; Lindorff-Larsen, K.; Dobson, C. M.; Karplus, M.; Vendruscolo, M. J. Mol. Biol. 2005, 352, 495.
-
(2005)
J. Mol. Biol.
, vol.352
, pp. 495
-
-
Paci, E.1
Lindorff-Larsen, K.2
Dobson, C.M.3
Karplus, M.4
Vendruscolo, M.5
-
36
-
-
0036138028
-
-
Ferrara, P.; Apostolakis, J.; Caflisch, A. Proteins 2002, 46, 24.
-
(2002)
Proteins
, vol.46
, pp. 24
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
39
-
-
0043141427
-
-
Guo, Y.; Shalashilin, D. V.; Krouse, J. A.; Thompson, D. L. J. Chem. Phys. 1999, 110, 5521.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 5521
-
-
Guo, Y.1
Shalashilin, D.V.2
Krouse, J.A.3
Thompson, D.L.4
-
40
-
-
0009704365
-
-
Guo, Y.; Shalashilin, D. V.; Krouse, J. A.; Thompson, D. L. J. Chem. Phys. 1999, 110, 5514.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 5514
-
-
Guo, Y.1
Shalashilin, D.V.2
Krouse, J.A.3
Thompson, D.L.4
-
43
-
-
84906381461
-
-
Moroni, D.; van Erp, T. S.; Bolhuis, P. G. Phys. Rev. 2005, 71, 5.
-
(2005)
Phys. Rev.
, vol.71
, pp. 5
-
-
Moroni, D.1
Van Erp, T.S.2
Bolhuis, P.G.3
-
44
-
-
34547648612
-
-
Allen, R. J.; Frenkel, D.; ten Wolde, P. R. J. Chem. Phys. 2006, 124, 16.
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 16
-
-
Allen, R.J.1
Frenkel, D.2
Ten Wolde, P.R.3
-
46
-
-
84906383630
-
-
Escobedo, F. A.; Borrero, E. E.; Araque, J. C. J. Phys.: Condens. Matter 2009, 21, 23.
-
(2009)
J. Phys.: Condens. Matter
, vol.21
, pp. 23
-
-
Escobedo, F.A.1
Borrero, E.E.2
Araque, J.C.3
-
47
-
-
84906371877
-
-
Forney, M. W.; Janosi, L.; Kosztin, I. Phys. Rev. E 2008, 78, 9.
-
(2008)
Phys. Rev. e
, vol.78
, pp. 9
-
-
Forney, M.W.1
Janosi, L.2
Kosztin, I.3
-
50
-
-
70349610330
-
-
Glowacki, D. R.; Marsden, S. P.; Pilling, M. J. J. Am Chem. Soc. 2009, 131, 13896.
-
(2009)
J. Am Chem. Soc.
, vol.131
, pp. 13896
-
-
Glowacki, D.R.1
Marsden, S.P.2
Pilling, M.J.3
-
51
-
-
60049087591
-
-
Glowacki, D. R.; Reed, S. K.; Pilling, M. J.; Shalashilin, D. V.; Martinez-Nunez, E. Phys. Chem. Chem. Phys. 2009, 11, 963.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 963
-
-
Glowacki, D.R.1
Reed, S.K.2
Pilling, M.J.3
Shalashilin, D.V.4
Martinez-Nunez, E.5
-
53
-
-
33646935697
-
-
Olsson, M. H. M.; Parson, W. W.; Warshel, A. Chem. Rev. 2006, 106, 1737.
-
(2006)
Chem. Rev.
, vol.106
, pp. 1737
-
-
Olsson, M.H.M.1
Parson, W.W.2
Warshel, A.3
-
55
-
-
0037038372
-
-
Snow, C. D.; Nguyen, H.; Pande, V. S.; Gruebele, M. Nature 2002, 420, 102.
-
(2002)
Nature
, vol.420
, pp. 102
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
56
-
-
0037478676
-
-
Paci, E.; Cavalli, A.; Vendruscolo, M.; Caflisch, A. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 8217.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 8217
-
-
Paci, E.1
Cavalli, A.2
Vendruscolo, M.3
Caflisch, A.4
-
61
-
-
23444454552
-
-
Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A;.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26, 1668.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
62
-
-
67650500988
-
-
Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Gui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, G B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. J. Comput. Chem. 2009, 30, 1545.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545
-
-
Brooks, B.R.1
Brooks III, C.L.2
Mackerell Jr., A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Gui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, G.B.26
Pu, J.Z.27
Schaefer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
63
-
-
27344454932
-
-
Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. J. Comput. Chem. 2005, 26, 1701.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
64
-
-
27344436659
-
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
|