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Steered molecular dynamics - umbrella samling
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1
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27
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December 8, 2025
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electric filed with position restraint
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0
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19
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December 3, 2025
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Free energy peturbation mdp file settings for solvation free energy calculation
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3
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41
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December 3, 2025
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Simulating a Reverse Transcriptase complex with RNA, DNA
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1
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12
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December 1, 2025
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Box explodes using NPT.mdp
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2
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40
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November 26, 2025
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Query regarding making all .mdp files for ionization, equllibration, energy minimization
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2
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29
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November 25, 2025
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Position restraints causing mdrun to stall on step 0
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3
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43
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November 17, 2025
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How does hydrogen mass repartitioning with an increased time step of 4 fs affect other mdp options?
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16
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1051
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November 6, 2025
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Free-energy on virtual sites only (or vice versa)
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2
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54
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October 29, 2025
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Constraint in stochastic dynamics
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3
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45
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October 29, 2025
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Umbrella sampling PMFs with additional restraints
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0
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41
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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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28
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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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20
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October 10, 2025
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Performance of SMD simulation
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1
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37
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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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32
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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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47
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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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66
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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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29
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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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139
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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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1234
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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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55
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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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88
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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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37
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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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31
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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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39
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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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50
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August 14, 2025
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Maxwell distribution gen_t
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6
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51
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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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25
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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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80
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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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50
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August 6, 2025
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