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What is the standard state of free energy calculations on GROMACS?
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3
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56
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September 18, 2023
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Relaxing a harmonic restraint using restraint-lambda
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0
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81
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August 22, 2023
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Scaling position restraints with restraint-lambdas
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9
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516
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July 25, 2023
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Free energy landscape calculation using gmx sham module
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2
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1247
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July 18, 2023
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GPU and perturbed non-bonded forces
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3
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78
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June 22, 2023
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Non equilibrium alchemical transformations - Creation - couple-intramol=no
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4
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1368
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June 3, 2023
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Umbrella sampling - WHAM analysis
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0
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314
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April 13, 2023
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What is the epsilon value for softcore LJ when C6 or C12 is zero?
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10
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139
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April 13, 2023
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Post-doc position open for one year in my lab in Nantes, France
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0
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186
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April 7, 2023
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How do solvation free energy calculation work?
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2
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131
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March 22, 2023
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Running AWH with polymer end to end distance as the reaction coordinate
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1
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114
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March 20, 2023
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Simulations with free energy calculations on GPU is several time slower than normal simulations
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4
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562
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January 2, 2023
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Error triggered by the use of couple-intramol=no
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1
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273
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December 9, 2022
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TI - Free Energy - couple-intramol=no
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14
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735
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December 8, 2022
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Free energy perturbation for part of a molecule
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2
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242
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November 17, 2022
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Issue with lambda = 1 during free energy calculations
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5
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251
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October 25, 2022
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Atoms collapse while free energy simulation
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0
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145
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October 24, 2022
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System blowing up in decoupled ligand (in protein complex) simulation for ABFE calculations
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9
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491
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October 11, 2022
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Free energy calc gives "WARNING: Some of these results violate the Second Law of Thermodynamics"
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5
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821
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September 6, 2022
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Standard error on AWH free energy estimate?
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6
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306
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June 7, 2022
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Cannot perform free energy calculations due to the solvent (not the solute) possessing CBT bonds?
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1
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307
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March 8, 2022
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Recalculate potential energy according to a different topology
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3
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193
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February 2, 2022
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Using FEP in implicit solvent
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1
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363
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January 26, 2022
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How to Calculate the linear interaction energy
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16
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1565
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January 7, 2022
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Free energy calculation at lambda=1 vs regular MD give different RDFs
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3
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347
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December 11, 2021
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Test FEP output file
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1
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235
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December 9, 2021
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Calculate the solvation free energy
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1
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473
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November 17, 2021
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Fast pulling ligand method for free energy
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1
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211
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November 9, 2021
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Fast pulling ligand
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1
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177
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November 9, 2021
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AWH FEP mdp options
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5
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999
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September 3, 2021
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