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Expanded ensemble: Performance impact of perturbing more atoms
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4
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12
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January 23, 2025
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What is the proper way of doing Free energy calculations in gromacs?
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1
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18
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January 22, 2025
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Free energy of mutation - example on an amino acid
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0
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28
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January 6, 2025
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Analysis of AWH simulations
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2
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46
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November 18, 2024
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Cutoff-dependent deviations in free energy for force switching and potential shifting
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3
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58
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October 23, 2024
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Applying restraining for a ligand in a binding pocket in ABFE calculation
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1
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23
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October 18, 2024
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Free energy, annihilation: charged ligand
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7
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89
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October 17, 2024
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Is gmx bar reading dH/dl for masses?
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8
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58
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October 15, 2024
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Restraints free energy
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1
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67
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September 21, 2024
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Free energy annihilation chromophore in scaffold
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6
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32
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September 20, 2024
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MDP files for DNA free energy perturbation (equilibrium)
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0
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21
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September 18, 2024
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Mutating residue, free energy
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3
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81
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September 18, 2024
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Fatal error: Perturbed masses or constraints are not supported by rerun
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1
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30
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September 10, 2024
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Charged solute, thermodynamic integration, couple-intramol = yes
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0
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46
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September 1, 2024
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Gmx bar output - central limit theorem
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0
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42
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August 30, 2024
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Gmx bar output: interpretation of +/- error estimations
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0
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40
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August 30, 2024
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PMF of interaction between a positive ion and a negative ion
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0
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19
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August 27, 2024
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Pull code for a single window
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3
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21
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August 22, 2024
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Ligand binding free energy in a burried pocket
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8
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117
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August 21, 2024
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Gaussian quadrature in thermodynamic integration
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0
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35
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August 20, 2024
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Solvation free energy calculation
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2
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83
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August 13, 2024
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Free energy calculation with fixed relative position
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2
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47
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August 12, 2024
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TI - Free Energy - couple-intramol=no
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35
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2475
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August 6, 2024
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How to decouple the Lennard-Jones (LJ) interaction between two particular atoms in a same molecule?
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0
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26
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July 11, 2024
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Problems in PMF curve of AquaporinZ after umbrella sampling
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18
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370
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July 1, 2024
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Incorrect relative solvation free energy values using single topology alchemical transformation
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8
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316
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May 5, 2024
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Simulations with free energy calculations on GPU is several time slower than normal simulations
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6
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993
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April 26, 2024
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Why is coulomb SR energy different sign using different forcefields?
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13
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504
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April 11, 2024
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Dummy Alchemical Ions in Gromacs
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0
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220
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April 2, 2024
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MMPBSA value is a possitive
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4
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261
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April 2, 2024
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