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Membrane Protein ligand simulation
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9
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188
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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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12
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July 6, 2025
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Segmentration Fault and to small of a timestep problem from a Amber built system
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19
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547
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November 11, 2024
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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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14
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July 3, 2025
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74% GPU utilization and 2/3 power usage on WSL2
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1
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26
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July 2, 2025
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Simulation with a 3 fs timestep
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0
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22
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June 30, 2025
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During Energy minimization error "Listed nonbonded interaction between particles 4778 and 4797 at d"
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1
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15
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June 28, 2025
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Using -membed option in gromacs
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0
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24
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June 25, 2025
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LINCS Warning or Freeze Behavior Depends on GROMACS Version
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0
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15
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June 20, 2025
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Unexpected geometry change when combing `freezegrps` with `constraints` and running MD
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6
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33
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June 19, 2025
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Membrane protein simulation
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1
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22
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June 18, 2025
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GROMACS cant detect GPU (AMD)
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7
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126
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May 27, 2025
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Unusual RMSD of ligand-protein
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6
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92
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May 23, 2025
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Mdrun crashes with some md parameter during NPT (gmx compiled for rocm,AdaptiveCPP)
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8
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72
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May 22, 2025
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Error While running npt equillibration of last frames extracted form complex
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0
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14
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May 22, 2025
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System has non-zero total charge: -1.000000
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1
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24
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May 19, 2025
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ERROR 1 [file dd.itp, line 198]: No default Proper Dih. types
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0
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19
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May 19, 2025
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Error ABFE calculation
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0
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17
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May 19, 2025
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Splitting 100ns Gromacs runs into 25ns smaller chunks
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0
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32
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May 19, 2025
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RESNAME error while using cgenff_charmm2gmx script
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1
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237
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May 18, 2025
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MSD changes with .xtc timestep
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0
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22
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May 17, 2025
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Segmentation fault or cuda error #700 during eABF/WTM-eABF calculations
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0
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9
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May 17, 2025
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Ligand Preparation for CHARMM36ff - Issue with halogens (Cl, Br)
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0
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22
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May 13, 2025
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Rerun xtc file generates different potential energies compared to original data
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2
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24
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May 14, 2025
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Need help minimising a backmapped system (I used backward method)
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0
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13
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May 12, 2025
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Update Groups Can't Be Created for GROMACS2024
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2
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37
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May 6, 2025
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Fixing coordinates of a chain after simulation
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6
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48
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May 4, 2025
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SMD output files and interpretation
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0
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11
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May 2, 2025
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RTX 5070 Not Utilized
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2
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175
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April 30, 2025
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How do we omit the positive/negative strain at zero stress?
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1
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29
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April 29, 2025
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