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RMSD for Protein-Ligand complex
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2
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1002
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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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41
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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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75
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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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49
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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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64
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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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61
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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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98
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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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Use of refcoordscaling in CHARMM and MARTINI
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0
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28
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July 7, 2026
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Workstation options
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2
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141
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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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114
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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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52
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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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92
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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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121
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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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62
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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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46
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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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99
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July 1, 2026
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Efficient Workflow for Multiple Modified Residues
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2
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61
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July 1, 2026
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Ligand jumping around during GROMACS MD simulation after CHARMM-GUI setup – PBC issue or system prep
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1
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44
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June 26, 2026
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Gromacs 2025.4 + Plumed 2.10 Installation issue
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0
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54
|
June 26, 2026
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Trying to perturb a torsion with multiple terms
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1
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35
|
June 25, 2026
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Protein small molecule simulation
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3
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88
|
June 25, 2026
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Temperature coupling
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3
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112
|
June 24, 2026
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Standard publishable preprocessing of AlphaFold3 complex structures for GROMACS MD simulations
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0
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70
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June 24, 2026
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Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding
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1
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46
|
June 24, 2026
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Fatal Error: no domain decomposition for rank 4, min cell size 1.776 nm
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1
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54
|
June 24, 2026
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GROMACS pdb2gmx Warning: Missing Atoms (H and O) in AlphaFold3-Derived TCR–pMHC Structure
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1
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41
|
June 24, 2026
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TIP4P/2005 water model
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2
|
622
|
June 22, 2026
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