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Title: Simulation Parameters used in the Study titled "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method" Open Access Deposited
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To Cite this Work:
(2017). Simulation Parameters used in the Study titled "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/Z2M906KK
(2017). Simulation Parameters used in the Study titled "Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/Z2M906KK
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Files (Count: 2; Size: 31.7 KB)
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Simulation Parameters_Readme.txt | 2017-08-16 | 2018-12-07 | 1.36 KB | Open Access |
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Simulation Parameters.xlsx | 2017-08-16 | 2018-12-07 | 30.4 KB | Open Access |
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Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method
Ming Huang, Wenjun Huang, Fei Wen, and Ronald G. Larson*
Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109-2136
*rlarson@umich.edu
Parameters Used in the Umbrella Sampling Simulations
We provide the parameters used in Umbrella Sampling simulations carried using GROMACS 4.6.5 reported in our study (DOI: 10.1002/jcc.24845), namely the set positions (x) and spring constants (K) for each window in simulations. Tab 1 lists the names of the peptides and their corresponding sequences. Tab 2-12 lists the parameters. The title of each simulation in Tab 2-12 follows the convention ˇ°Force Field_Peptide Name_Reaction Coordinateˇ±. Note two reaction coordinates are employer, namely center-of-mass (COM) and peeling from one peptide end (peel). Those marked with ˇ°*ˇ± are windows repaired by increasing the spring constant; those marked with ˇ°**ˇ± are windows added to ensure sufficient overlap, where overlap was inadequate in the original histograms. These parameters can be supplied to GROMACS 4.6.5 via the following commends in mdp file: pull: umbrella; pull-geometry: distance; pull-coord1-init: set_distance_in_table; pull-coord1-k: K_value_in_table;
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