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Help with simulated annealing of a small peptide
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1
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93
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February 20, 2024
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PACKMOL and gmx2pdb
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0
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104
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February 20, 2024
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Implausible values in free energy calculations
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4
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198
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February 16, 2024
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Tabulated non-bonded interactions
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6
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115
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February 15, 2024
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Request for Free Energy Integration Files Using Dummy Atoms
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3
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145
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February 3, 2024
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Issue of High Potential Energy on Running Minimization
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9
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243
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February 1, 2024
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LINCS warning during energy minimizations
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8
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1270
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January 24, 2024
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How to Calculate the linear interaction energy
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17
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2356
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January 20, 2024
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How can we change the pH of a solution?
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1
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191
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January 18, 2024
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Mdp files of Charmm-gui server
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8
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622
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January 18, 2024
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Steered MD settings
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2
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129
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January 16, 2024
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Optimal Trajectory Saving for Accurate H-bond Lifetime Calculation
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0
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92
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January 14, 2024
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Trying to mimic biophysical experiment concentration
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0
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115
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December 25, 2023
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Simulation Breaks the system (separates both the chains of the Antibody)
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10
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866
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December 24, 2023
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How to avoid the error "One or more water molecules cannot be settled"
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0
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186
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December 22, 2023
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RMSD curve of the protein of the lipid bilayer simulation
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0
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176
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December 21, 2023
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Solvation Energy calculation
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34
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735
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December 21, 2023
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Using AWH for bilayer permeability
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15
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565
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December 21, 2023
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Constant pH MD
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0
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205
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December 21, 2023
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Invalid input values
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0
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136
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December 18, 2023
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AWH very large free energy barriers
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13
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231
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December 18, 2023
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Position restraints in mdp file
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2
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515
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December 18, 2023
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Mdp parameters for non-bonded interaction using the AMBER force field
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7
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2682
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December 16, 2023
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Roto-translational constraints in GROMACS
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0
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133
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December 15, 2023
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NOTE 1 [file NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
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2
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1264
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December 15, 2023
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Error in MD simulation
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0
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248
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December 14, 2023
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How to set awh1-dim1-diffusion and awh1-error-init properly
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4
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205
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December 12, 2023
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Lincs warnings in NVT equilibration runs for alchemical calculations
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0
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231
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December 9, 2023
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Inculding a replusion force between selected atoms for sMD
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1
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119
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December 5, 2023
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Regarding the topology is not created in the ATB server. how to overcome this issue?
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0
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129
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December 1, 2023
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