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Umbrella sampling PMFs with additional restraints
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0
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13
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October 20, 2025
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Water accumulation in slab geometry
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0
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6
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October 20, 2025
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Colvars: get topol chain names to match make_ndx
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1
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19
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October 10, 2025
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Performance of SMD simulation
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1
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28
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October 10, 2025
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How to simulate a cyclic protein with AMBER99SB ff?
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1
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21
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October 9, 2025
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what should do with zink-protein.pdf to get topology file?
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5
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41
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October 7, 2025
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Inaccurate thermostatting when simulating MD water
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1
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40
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October 4, 2025
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Applying no cut off can affect the result?
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1
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26
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September 23, 2025
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Pressure scaling more than 1%. This may mean your system is not yet equilibrated
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5
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74
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September 15, 2025
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Energy minimization with position restraints in charmm-gui mdp file
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5
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1219
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September 13, 2025
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Comm-mode setting in applied field simulation in membrane-protein complex
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3
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43
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September 9, 2025
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RMSD graph after protein protein md simulation
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4
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69
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September 8, 2025
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Membrane artefacts when pulling membrane proteins together using Martini forcefield
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3
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24
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September 4, 2025
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Assistance Needed: "Atomtype F not found" Error in GROMACS Minimization with TFE Solvent
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1
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19
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September 3, 2025
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Unexplained calculation stalling during density fit
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2
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32
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August 25, 2025
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Pressure decreasing after npt equilibration
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2
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41
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August 14, 2025
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Maxwell distribution gen_t
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6
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42
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August 12, 2025
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Mdrun log file error Large VCM(group MEMB)
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1
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22
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August 11, 2025
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Osmotic pressure simulations using the pull code
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6
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65
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August 7, 2025
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Value too high for SFE (charmm-gui files)
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5
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40
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August 6, 2025
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Minimization of a membrane-peptide complex
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0
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22
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August 2, 2025
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How to read in an xyz vector from the .mdp file
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1
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42
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July 28, 2025
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Pressure Scaling more than 1% and volume fluctuations
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1
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57
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July 25, 2025
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Issues when equilibrating a membrane system with 2024.4 (not present in 2023.3)
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1
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29
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July 22, 2025
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Gen_vel=no and continuation=false
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3
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193
|
July 22, 2025
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Homocysteine covalently bonded with a protein MD simulation how to perform
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0
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33
|
July 21, 2025
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Computational Electrophysiology Setup with GROMACS (.mdp file)
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3
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262
|
July 19, 2025
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Frozen beads - no movements
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2
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29
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July 7, 2025
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Restraining Solvent Molecules Under an Ice Slab
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0
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27
|
July 6, 2025
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Clarification on Iodide Parameters for CHARMM36 in GROMACS
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0
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30
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June 30, 2025
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