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Advice on CGenFF penalty scores for a large, DFT-optimised molecule
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4
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122
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July 29, 2026
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Preprocessing error with CGenFF 5.0 topology: unsupported multiple CHARMM type-9 dihedral parameters
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0
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27
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July 29, 2026
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How create Charmm36 topology parameters for glycans
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2
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78
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July 28, 2026
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Parametrization of pyroglutamate
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2
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73
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July 28, 2026
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AWH convergence for a charged ligand permeating a bilayer
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5
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98
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July 28, 2026
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Trans to cis confirmation at NVT step
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0
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33
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July 28, 2026
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Regressiontests/complex tests fail with intelmpi GHROMACS build
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1
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57
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July 27, 2026
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How to simulate EDLC (Electrochemical Double Layer)?
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1
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172
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July 24, 2026
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Simulation of a dizinc metallo protein
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6
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606
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July 24, 2026
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When is trajectory preprocessing (whole/cluster/nojump/center) actually required for analysis?
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2
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105
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July 24, 2026
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Umbrella sampling simulation pulling towards periodic box using martini 3 forcefield
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3
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66
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July 23, 2026
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X2top not generating listed interactions correctly
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1
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55
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July 23, 2026
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Simulating an Infinite polymer across boundaries
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1
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56
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July 23, 2026
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"No default Per. Imp. Dih. types" when using amber14sb_parmbsc1_cufix force field
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0
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34
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July 21, 2026
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How to remove duplicate frames
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2
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47
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July 20, 2026
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Gmx order for unsaturated AII-Atom lipid chains
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3
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425
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July 18, 2026
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DNA and protein grouping for RMSD calculations
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0
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43
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July 17, 2026
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Issue with ligand preparation in CGENFF
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0
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44
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July 15, 2026
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Multiple gmx processes on GPU(s) ran too slowly
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10
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220
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July 13, 2026
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Simulation of whole yeast ribosome to study single residue substitution in core RP
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0
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27
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July 13, 2026
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RMSD for Protein-Ligand complex
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2
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997
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July 13, 2026
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Trajectory preprocessing in peptide self-assembly simulations
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0
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40
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July 12, 2026
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gmx_MMPBSA for big molecule
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1
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72
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July 10, 2026
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PBC correction for ionisable lipid–lipid bilayer system (GROMACS 2025.4)
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0
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48
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July 10, 2026
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GROMACS Courtesy
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0
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45
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July 10, 2026
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TIP4P/Ice .itp File
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0
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35
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July 9, 2026
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gmx_MMPBSA error in Steered Molecular dynamics simulation trajectory
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1
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62
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July 9, 2026
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G_mmpbsa for the gromacs 2025 versions
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1
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55
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July 9, 2026
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Atoms not completely removed by convert-tpr
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3
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92
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July 8, 2026
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PBC wrapping for Protein-Ligand-Surface system
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0
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32
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July 7, 2026
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