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IFT in CG simulation using MARTINI 3.0
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1
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46
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June 12, 2026
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Charmm36 and lj-pme setting
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2
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86
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June 12, 2026
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Shear Viscosity Calculation for Isotropic Molecules
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7
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91
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June 9, 2026
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Deform by Gromacs to apply shear rate
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8
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2591
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June 9, 2026
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ForceField for Intrisically disordered protein
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14
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144
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June 8, 2026
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Statistical Analysis Method for Peak force and total work in Steered molecular dynamics
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3
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67
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June 4, 2026
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What if the protein contains mutations and missing residues?
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2
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85
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June 4, 2026
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Gmx anaeig problematic error "Dimensions in the eigenvector files don't match"
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4
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54
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June 3, 2026
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Modified dihedral notation
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6
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72
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June 3, 2026
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Convert amber to gromacs
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0
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50
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June 2, 2026
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Force Field-angle
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2
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40
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June 1, 2026
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Is there a way to perform simulations with less standard addatives?
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3
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51
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June 1, 2026
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Calculating the free energy of binding using AWH approach
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8
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149
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May 28, 2026
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Box changing shape after equilibration
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8
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130
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May 26, 2026
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GROMACS 2026.3-dev on gfx1201 (RX 9070 XT) - Device detection failure
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5
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119
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May 26, 2026
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DCLE diffuse into Bulk solution from membrane after 1.8 ns equilbration in HMMM (Charmm-Gui)
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0
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31
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May 26, 2026
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Possible inconsistency when mixing GROMACS 2023.1 and 2025.x for umbrella sampling workflows
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2
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59
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May 23, 2026
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For those who wanna build on Windows with Visual Studio 2026
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1
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61
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May 20, 2026
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Simulation box size?
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7
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117
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May 19, 2026
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Water surface tension
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12
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202
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May 19, 2026
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Gromacs installation on Fugaku ARM (A64FX) Node with Fujitsu MPI
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8
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68
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May 19, 2026
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Excluded distance larger than cutoff in ligand with virtual site
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22
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670
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May 19, 2026
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COM motion removal during NVT simulation with electric field
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5
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90
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May 19, 2026
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Centering a molecule that crosses periodic boundaries — single-atom trick
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1
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57
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May 18, 2026
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How to solve inconsistent shifts over periodic boundaries in protein-dna run in minimization step?
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11
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3073
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May 17, 2026
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Divalent ion parameterization in GROMACS
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1
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48
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May 13, 2026
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Segmentation fault without further information
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3
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59
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May 13, 2026
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Colvars: Error: keyword "customfunction" is not supported
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3
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190
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May 12, 2026
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Details of viscosity estimation (gmx energy -vis)
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6
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1298
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May 11, 2026
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Mindist usage on multichain systems
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0
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19
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May 11, 2026
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