Steered molecular dynamics

Stepaniants et al., 1997] Stepaniants, S., Izrailev, S., and Schulten, K. Extraction of lipids from phospholipid membranes by steered molecular dynamics. J. Mol. Model. 3 (1997) 473-475... 

Wriggers and Schulten, 1998] Wriggers, W., and Schulten, K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Biophys. J. Submitted. 

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

It is interesting to note that the free energy profiles obtained with ABF are essentially identical to those derived by Park et al. [53] from a reversible, 200-ns steered molecular dynamics simulation and from a set of 100 shorter runs, pulling very... 

Lu, H. Isralewitz, B. Krammer, A. Vogel, V. Schulten, K., Unfolding of titin immunoglobulin domains by steered molecular dynamics simulation, Biophys. J. 1998, 75, 662-671... 

Isralewitz, B. Gao, M. Schulten, K., Steered molecular dynamics and mechanical functions of proteins, Cure Opin. Struct. Biol. 2001,11, 224—230... 

Lu, H. Schulten, K., Steered molecular dynamics simulations of force-induced protein domain unfolding, Proteins Struct. Funct. Gene. 1999, 35, 453 163... 

Park, S. Khalili-Araghi, F. Tajkhorshid, E. Schulten, K., Free energy calculation from steered molecular dynamics simulations using Jarzynski s equality, J. Chem. Phys. 

Izrailev, S. Stepaniants, S. Isralewitz, B. Kosztin, D. Lu, H. Molnar, F. Wriggers, W. Schulten, K. Steered molecular dynamics, in Computational Molecular Dynamics Challenges, Methods, Ideas, Deuflhard, P. Hermans, 1. Leimkuhler, B. Mark, A. E. Skeel, R. Reich, S., Eds., vol. 4, Lecture Notes in Computational Science and Engineering. Springer Verlag Berlin, 1998, pp. 39-65. 

Monticelli, L., Robertson, K.M., MacCallum, J.L., Tieleman, D.P. Computer simulation of the KvAP voltage-gated potassium channel steered molecular dynamics of the voltage sensor. FEBS Lett. 2004, 564, 325-32. 

S. Park and K. Schulten, Calculating potentials of mean force from steered molecular dynamics simulation. J. Chem. Phys. 13, 5946—5961 (2004). 

Ludemann SK, Lounnas V, Wade RC. How do substrates enter and products exit the buried active site of cytochrome P450cam 2. Steered molecular dynamics and adiabetic mapping of substrate pathways. J Mol Biol 2000 303 813-830. 

Key words Molecular dynamics, Poisson-Boltzmann, Generalized Born, Linear interaction energy, Binding free energy, Periodic boundary conditions, Steered molecular dynamics... 

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