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Do we need position restraints for deformation simulations?
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0
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8
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October 7, 2024
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Running an NPT simulation after NVT (domain decomposition error)
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3
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15
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October 7, 2024
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Breaking of the molecular structure after energy minimization
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3
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8
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October 4, 2024
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SD integrator vs MD integrator
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6
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65
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September 30, 2024
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Position restraints for Umbrella sampling simulation of membrane protein-ligand
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5
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30
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September 30, 2024
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Reference coordinate scaling during umbrella sampling simulations?
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1
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17
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September 30, 2024
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Acceleration
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2
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33
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September 27, 2024
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GRINN Energy Scoring
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4
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379
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September 26, 2024
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Yeh-Berkovitz correction
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3
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10
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September 26, 2024
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How to Calculate Energies for "Specific" Atoms?
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1
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14
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September 25, 2024
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Bumpy energy profile from PMF
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7
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43
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September 24, 2024
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Force field for Magnesium
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0
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13
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September 24, 2024
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Graphene Piston
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11
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96
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September 23, 2024
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LJ-PME with user defined non-bonded parameters
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1
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878
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September 21, 2024
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How to understand the output after pulling force is applied?
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11
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74
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September 20, 2024
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Investigation of Thermomechanical Properties and Vibration Behavior in a Highly Crosslinked Polymer
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0
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8
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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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13
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September 18, 2024
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How to make a molecule completely rigid in gromacs without using a lot of constraints?
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0
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9
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September 16, 2024
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How to apply constant pull force at two ends of a molecule?
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2
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46
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September 10, 2024
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Timestep in gromacs
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4
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43
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September 5, 2024
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Pull-coord1-geometry = direction vs pull-coord1-geometry = direction-periodic
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3
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35
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September 3, 2024
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Charged solute, thermodynamic integration, couple-intramol = yes
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0
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33
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September 1, 2024
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Energy Minimization of protein (PDB)
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3
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38
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August 30, 2024
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Error in NPT Equilibration for Protein Ligand Complex MD Tutorial
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3
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45
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August 28, 2024
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Confusing Density from NPT run
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8
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46
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August 28, 2024
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System equillibrating but no big changes in membrane
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4
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20
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August 28, 2024
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Box volume gradually increased with 0.01 fs time step
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3
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25
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August 26, 2024
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Issue of High Potential Energy on Running Minimization
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22
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624
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August 20, 2024
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NPT equilibration with LINCS and frozen solute
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1
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25
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August 20, 2024
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Cutoff-scheme and intermolecular interactions
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1
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36
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August 20, 2024
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