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Pore water generation during membrane protein simulations
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0
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9
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August 16, 2025
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Normal Mode Analysis – Minimization Doesn’t Reach Target emtol & Zero Eigenfrequencies
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7
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49
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August 15, 2025
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Placing a mixture of phospholipids all together closer together in a bilayer
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3
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15
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August 15, 2025
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Charm gui equilibration steps
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7
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41
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August 12, 2025
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NVT/NPT runs
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6
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61
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August 12, 2025
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Pull code on a long filament
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7
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50
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August 12, 2025
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I want to compare WT vs mutant protein KD to DNA (and possibly inhibitors)... I have questions
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3
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21
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August 9, 2025
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Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
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1
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14
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August 9, 2025
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How do I correctly re-wrap DCLE tail-solvent and lipids in an HMMM trajectory?
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0
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9
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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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14
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August 2, 2025
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Modifying topol.top with each step of peptide insertion over membrane from CHARMM-GUI
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2
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32
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August 2, 2025
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Problem with gromacs script generetated with charmm-gui
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3
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28
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July 30, 2025
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Insert the simulation box
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0
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12
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July 29, 2025
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Problem with adding ions
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1
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12
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July 28, 2025
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High LJ (SR) in graphene sheet minimization
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0
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9
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July 28, 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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28
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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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181
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July 22, 2025
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.pdb and .top file
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0
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17
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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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24
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July 21, 2025
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Computational Electrophysiology Setup with GROMACS (.mdp file)
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3
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246
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July 19, 2025
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Free Energy Calculation of Tryptophan
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1
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25
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July 18, 2025
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Equilibration of new lipid model
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0
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9
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July 16, 2025
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How to create restrained file for sol
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0
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15
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July 15, 2025
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Flat-bottom position restraints on water molecules
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5
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28
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July 7, 2025
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How to simulate the specific residues by mentioning their position in the sequence?
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0
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16
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July 3, 2025
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How to prepare nucleotides for MD simulation?
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0
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23
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June 26, 2025
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Backmapping from coarse grain to all atom
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3
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68
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June 26, 2025
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Forcefield to simulate RNA molecules containing modifications with GROMACS and amber ff
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2
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401
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June 20, 2025
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Is it possible to use an eam potential?
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2
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26
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June 5, 2025
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