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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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94
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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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62
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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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48
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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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54
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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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31
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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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420
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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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41
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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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38
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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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209
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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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25
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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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985
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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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39
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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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66
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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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47
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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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34
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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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57
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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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51
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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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77
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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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28
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July 7, 2026
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Use of refcoordscaling in CHARMM and MARTINI
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0
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26
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July 7, 2026
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Workstation options
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2
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132
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July 7, 2026
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Can CGenFF-generated partial charges differ significantly from QM-derived CHELPG (ESP) charges?
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2
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96
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July 5, 2026
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RMSD analysis of the Protein-Ligand simulation
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0
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50
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July 5, 2026
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How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction
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1
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84
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July 4, 2026
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How to deal with Zn ion in Zinc finger protein
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3
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104
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July 3, 2026
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GROMACS 2026.2 duplicate type-9 dihedral errors with CHARMM36-feb2026 and CGenFF 5.0
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1
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51
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July 3, 2026
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How to determine b0 and kb in Zn-coordinated bond
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0
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42
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July 2, 2026
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How to generate a MOL2 ligand file with the correct docking pose, full hydrogens, and physiological
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1
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82
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July 1, 2026
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