-
1
-
-
34548680131
-
-
Eds. Springer Series in Chemical Physics; Springer: Berlin
-
Pohorille, A., Chipot, C., Eds.; Free Energy Calculations; Springer Series in Chemical Physics; Springer: Berlin, 2007.
-
(2007)
Free Energy Calculations
-
-
Pohorille, A.1
Chipot, C.2
-
6
-
-
3142716857
-
-
Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120, 11919-11929
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
7
-
-
42149194240
-
-
Darve, E.; Rodríguez-Gómez, D.; Pohorille, A. J. Chem. Phys. 2008, 128, 144120
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 144120
-
-
Darve, E.1
Rodríguez-Gómez, D.2
Pohorille, A.3
-
9
-
-
41849093720
-
-
Babin, V.; Roland, C.; Sagui, C. J. Chem. Phys. 2008, 128, 134101
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 134101
-
-
Babin, V.1
Roland, C.2
Sagui, C.3
-
14
-
-
0030819348
-
-
Nakajima, N.; Nakamura, H.; Kidera, A. J. Phys. Chem. B 1997, 101, 817-824
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 817-824
-
-
Nakajima, N.1
Nakamura, H.2
Kidera, A.3
-
15
-
-
0034294024
-
-
Sugita, Y.; Kitao, A.; Okamoto, Y. J. Chem. Phys. 2000, 113, 6042-6051
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
20
-
-
84872159885
-
-
Nilmeier, J. E.; Crooks, G. E.; Minh, D. D. L.; Chodera, J. D. Proc. Natl. Acad. Sci. U.S.A. 2011, 108
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, pp. 108
-
-
Nilmeier, J.E.1
Crooks, G.E.2
Minh, D.D.L.3
Chodera, J.D.4
-
23
-
-
77954888698
-
-
SAGA BigJob: An Extensible and Interoperable Pilot-Job Abstraction for Distributed Applications and Systems, ACM
-
Luckow, A.; Lacinksi, L.; Jha, S. SAGA BigJob: An Extensible and Interoperable Pilot-Job Abstraction for Distributed Applications and Systems, The 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing; ACM, 2010; pp 135-144.
-
(2010)
The 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing
, pp. 135-144
-
-
Luckow, A.1
Lacinksi, L.2
Jha, S.3
-
24
-
-
84863959209
-
-
Towards a Common Model for Pilot-Jobs, ACM
-
Luckow, A.; Santcroos, M.; Weidner, O.; Merzky, A.; Maddineni, S.; Jha, S. Towards a Common Model for Pilot-Jobs, Proceedings of the 21st International Symposium on High-Performance Parallel and Distributed Computing, HPDC'12; ACM, 2012.
-
(2012)
Proceedings of the 21st International Symposium on High-Performance Parallel and Distributed Computing, HPDC'12
-
-
Luckow, A.1
Santcroos, M.2
Weidner, O.3
Merzky, A.4
Maddineni, S.5
Jha, S.6
-
25
-
-
84892576093
-
-
XSEDE '13
-
Radak, B. K.; Romanus, M.; Gallicchio, E.; Lee, T.-S.; Weidner, O.; Deng, N.-J.; He, P.; Dai, W.; York, D. M.; Levy, R. M.; Jha, S. Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery; XSEDE '13; 2013; pp 26:1-26:8.
-
(2013)
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery
, pp. 261-268
-
-
Radak, B.K.1
Romanus, M.2
Gallicchio, E.3
Lee, T.-S.4
Weidner, O.5
Deng, N.-J.6
He, P.7
Dai, W.8
York, D.M.9
Levy, R.M.10
Jha, S.11
-
29
-
-
84986519238
-
-
Kumar, S.; Bouzida, D.; Swendsen, R.; Kollman, P.; Rosenberg, J. J. Comput. Chem. 1992, 13, 1011-1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.3
Kollman, P.4
Rosenberg, J.5
-
32
-
-
0242677537
-
-
Shirts, M. R.; Bair, E.; Hooker, G.; Pande, V. S. Phys. Rev. Lett. 2003, 91, 140601
-
(2003)
Phys. Rev. Lett.
, vol.91
, pp. 140601
-
-
Shirts, M.R.1
Bair, E.2
Hooker, G.3
Pande, V.S.4
-
34
-
-
84859951540
-
-
Tan, Z.; Gallicchio, E.; Lapelosa, M.; Levy, R. M. J. Chem. Phys. 2012, 136, 144102
-
(2012)
J. Chem. Phys.
, vol.136
, pp. 144102
-
-
Tan, Z.1
Gallicchio, E.2
Lapelosa, M.3
Levy, R.M.4
-
37
-
-
65249137778
-
-
Maragakis, P.; van der Vaart, A.; Karplus, M. J. Phys. Chem. B 2009, 113, 4664-4673
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 4664-4673
-
-
Maragakis, P.1
Van Der Vaart, A.2
Karplus, M.3
-
38
-
-
84856754664
-
-
Hansen, N.; Dolenc, J.; Knecht, M.; Riniker, S.; van Gunsteren, W. F. J. Comput. Chem. 2012, 33, 640-651
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 640-651
-
-
Hansen, N.1
Dolenc, J.2
Knecht, M.3
Riniker, S.4
Van Gunsteren, W.F.5
-
39
-
-
84892619013
-
-
WHAM: The Weighted Histogram Analysis Method, version 2.0.4
-
Grossfield, A. WHAM: The Weighted Histogram Analysis Method, version 2.0.4. 2005.
-
(2005)
-
-
Grossfield, A.1
-
41
-
-
79951819347
-
-
Spiriti, J.; Binder, J. K.; Levitus, M.; van der Vaart, A. Biophys. J. 2011, 100, 1049-1057
-
(2011)
Biophys. J.
, vol.100
, pp. 1049-1057
-
-
Spiriti, J.1
Binder, J.K.2
Levitus, M.3
Van Der Vaart, A.4
-
46
-
-
84872130482
-
-
Lee, T.-S.; Radak, B. K.; Pabis, A.; York, D. M. J. Chem. Theory Comput. 2013, 9, 153-164
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 153-164
-
-
Lee, T.-S.1
Radak, B.K.2
Pabis, A.3
York, D.M.4
-
49
-
-
33947398571
-
-
Chodera, J. D.; Swope, W. C.; Pitera, J. W.; Seok, C.; Dill, K. A. J. Chem. Theory Comput. 2007, 3, 26-41
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 26-41
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Seok, C.4
Dill, K.A.5
-
50
-
-
58149231354
-
-
Chakravorty, D. K.; Kumarasiri, M.; Soudackov, A. V.; Hammes-Schiffer, S. J. Chem. Theory Comput. 2008, 4, 1974-1980
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1974-1980
-
-
Chakravorty, D.K.1
Kumarasiri, M.2
Soudackov, A.V.3
Hammes-Schiffer, S.4
-
51
-
-
80855148257
-
-
Spiriti, J.; Kamberaj, H.; Van Der Vaart, A. Int. J. Quantum Chem. 2012, 112, 33-43
-
(2012)
Int. J. Quantum Chem.
, vol.112
, pp. 33-43
-
-
Spiriti, J.1
Kamberaj, H.2
Van Der Vaart, A.3
-
56
-
-
0014857654
-
-
Akima, H. J. ACM 1970, 17, 589-602
-
(1970)
J. ACM
, vol.17
, pp. 589-602
-
-
Akima, H.1
-
60
-
-
0001568871
-
-
Apostolakis, J.; Ferrara, P.; Caflisch, A. J. Chem. Phys. 1999, 110, 2099-2108
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 2099-2108
-
-
Apostolakis, J.1
Ferrara, P.2
Caflisch, A.3
-
61
-
-
15544386773
-
-
Rosso, L.; Abrams, J. B.; Tuckerman, M. E. J. Phys. Chem. B 2005, 109, 4162-4167
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 4162-4167
-
-
Rosso, L.1
Abrams, J.B.2
Tuckerman, M.E.3
-
62
-
-
33644968698
-
-
Ensing, B.; De Vivo, M.; Liu, Z.; Moore, P.; Klein, M. L. Acc. Chem. Res. 2006, 39, 73-81
-
(2006)
Acc. Chem. Res.
, vol.39
, pp. 73-81
-
-
Ensing, B.1
De Vivo, M.2
Liu, Z.3
Moore, P.4
Klein, M.L.5
-
63
-
-
34247338100
-
-
Chodera, J. D.; Singhal, N.; Pande, V. S.; Dill, K. A.; Swope, W. C. J. Chem. Phys. 2007, 126, 155101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
65
-
-
84892609351
-
-
AMBER 12. University of California: San Francisco, CA
-
Case, D. A.. AMBER 12. University of California: San Francisco, CA, 2012.
-
(2012)
-
-
Case, D.A.1
-
66
-
-
0004016501
-
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
67
-
-
27344436659
-
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kaleé, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
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
Kaleé, L.9
Schulten, K.10
-
68
-
-
77953513118
-
-
Lindorff-Larsen, K.; Stefano, P.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Proteins 2010, 78, 1950-1958
-
(2010)
Proteins
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Stefano, P.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
71
-
-
0034513054
-
-
Henkelman, G.; Uberuaga, B. P.; Jónsson, H. J. Chem. Phys. 2000, 113, 9901-9904
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 9901-9904
-
-
Henkelman, G.1
Uberuaga, B.P.2
Jónsson, H.3
-
73
-
-
70350381537
-
-
Kästner, J.; Carr, J. M.; Keal, T. W.; Thiel, W.; Wander, A.; Sherwood, P. J. Phys. Chem. A 2009, 113, 11856-11865
-
(2009)
J. Phys. Chem. A
, vol.113
, pp. 11856-11865
-
-
Kästner, J.1
Carr, J.M.2
Keal, T.W.3
Thiel, W.4
Wander, A.5
Sherwood, P.6
-
74
-
-
84872164502
-
-
Radak, B. K.; Harris, M. E.; York, D. M. J. Phys. Chem. B 2013, 117, 94-103
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 94-103
-
-
Radak, B.K.1
Harris, M.E.2
York, D.M.3
-
75
-
-
0029011701
-
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Ferguson, D.M.5
Spellmeyer, D.C.6
Fox, T.7
Caldwell, J.W.8
Kollman, P.A.9
-
76
-
-
78651371352
-
-
Wong, K.-Y.; Lee, T.-S.; York, D. M. J. Chem. Theory Comput. 2011, 7, 1-3
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1-3
-
-
Wong, K.-Y.1
Lee, T.-S.2
York, D.M.3
-
79
-
-
0035826470
-
-
Lahiri, A.; Nilsson, L.; Laaksonen, A. J. Chem. Phys. 2001, 114, 5993-5999
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 5993-5999
-
-
Lahiri, A.1
Nilsson, L.2
Laaksonen, A.3
-
80
-
-
0041810451
-
-
Iannuzzi, M.; Laio, A.; Parrinello, M. Phys. Rev. Lett. 2003, 90, 238302
-
(2003)
Phys. Rev. Lett.
, vol.90
, pp. 238302
-
-
Iannuzzi, M.1
Laio, A.2
Parrinello, M.3
-
81
-
-
33748563197
-
-
Wang, J.; Gu, Y.; Liu, H. J. Chem. Phys. 2006, 125, 094907-094907
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 094907-094907
-
-
Wang, J.1
Gu, Y.2
Liu, H.3
-
82
-
-
33751558641
-
-
Babin, V.; Roland, C.; Darden, T. A.; Sagui, C. J. Chem. Phys. 2006, 125, 204909-204909
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 204909-204909
-
-
Babin, V.1
Roland, C.2
Darden, T.A.3
Sagui, C.4
-
83
-
-
34147094596
-
-
Lelievre, T.; Rousset, M.; Stoltz, G. J. Chem. Phys. 2007, 126, 134111-134111
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 134111-134111
-
-
Lelievre, T.1
Rousset, M.2
Stoltz, G.3
-
84
-
-
34548511984
-
-
Li, H.; Min, D.; Liu, Y.; Yang, W. J. Chem. Phys. 2007, 127, 094101-094101
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 094101-094101
-
-
Li, H.1
Min, D.2
Liu, Y.3
Yang, W.4
-
86
-
-
58149512801
-
-
Zheng, L.; Chen, M.; Yang, W. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 20227-20232
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 20227-20232
-
-
Zheng, L.1
Chen, M.2
Yang, W.3
-
88
-
-
79953802227
-
-
Min, D.; Chen, M.; Zheng, L.; Jin, Y.; Schwartz, M. A.; Sang, Q.-X. A.; Yang, W. J. Phys. Chem. B 2011, 115, 3924-3935
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 3924-3935
-
-
Min, D.1
Chen, M.2
Zheng, L.3
Jin, Y.4
Schwartz, M.A.5
Sang, Q.-X.A.6
Yang, W.7
-
90
-
-
84872168026
-
-
Arrar, M.; de Oliveira, C. A. F.; Fajer, M.; Sinko, W.; McCammon, J. A. J. Chem. Theory Comput. 2013, 9, 18-23
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 18-23
-
-
Arrar, M.1
De Oliveira, C.A.F.2
Fajer, M.3
Sinko, W.4
McCammon, J.A.5
|