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How to use the forum
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1
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3842
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October 28, 2020
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About the User discussions category
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0
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2034
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April 24, 2020
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The largest distance between non-perturbed excluded atoms ERROR
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9
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1496
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July 8, 2025
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Flat-bottom position restraints on water molecules
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5
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23
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July 7, 2025
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Frozen beads - no movements
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2
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19
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July 7, 2025
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How to write ryckaert-bellemans function in oplsaa force field
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0
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10
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July 7, 2025
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Membrane Protein ligand simulation
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9
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184
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July 7, 2025
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Removing water molecules from tpr file while conserving correct protein chain assignment
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0
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10
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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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Problems installing Gromacs 2025.2 with CUDA 12.9
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2
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37
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July 5, 2025
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Low density after NPT step (methanol/water mixture solvent)
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1
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21
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July 4, 2025
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Sbatch: error: Batch job submission failed: Node count specification invalid
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2
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13
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July 4, 2025
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Gromacs could find the Adaptivecpp/hipSYCL compiler
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3
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15
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July 3, 2025
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Guidance on Identifying CPU vs. GPU Bottlenecks in GROMACS Simulations
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8
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52
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July 3, 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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Simulation replicates and duration
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0
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11
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July 3, 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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12
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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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25
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July 2, 2025
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Building GROMACS on MI300X/MI325X using AdaptiveCpp and ROCM 6.33 failed due to incorrect GLIBCXX
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1
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19
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July 2, 2025
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Escape prime (') char in atom name for selection command
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5
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50
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July 2, 2025
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Negative eigen values while doing NMA of protein
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0
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7
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July 2, 2025
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Difficulty Maintaining Fe/S Cluster Geometry and Cysteine Coordination in CHARMM36
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0
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9
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July 2, 2025
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Charge Rounding-Off Error
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0
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13
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July 1, 2025
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Error in topology conversion from CGenFF
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0
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11
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July 1, 2025
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Running 100 ns GROMACS MD of a protein-ligand complex locally on Mac — is it feasible or worth it?
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4
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34
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July 1, 2025
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Distinct GROMACS versions yielded structural deviations, indicating version-specific dynamics
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3
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13
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June 30, 2025
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Clarification on Iodide Parameters for CHARMM36 in GROMACS
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0
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18
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June 30, 2025
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Simulation with a 3 fs timestep
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0
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19
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June 30, 2025
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Discrepancy in Tripeptide Aggregation Behavior Between GROMACS 2020.1 and 2023.3
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9
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52
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June 30, 2025
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Constrain receptor ligand
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0
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12
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June 28, 2025
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