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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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418
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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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40
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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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36
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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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195
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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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971
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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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36
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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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61
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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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44
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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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33
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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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50
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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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74
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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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25
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July 7, 2026
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Workstation options
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2
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130
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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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94
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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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49
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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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80
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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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101
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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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48
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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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38
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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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80
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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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53
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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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35
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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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46
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June 26, 2026
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Trying to perturb a torsion with multiple terms
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1
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31
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June 25, 2026
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Protein small molecule simulation
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3
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80
|
June 25, 2026
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