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Running gmx_mmpbsa for protein receptor - homodimer protein complex
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0
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50
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August 18, 2026
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hbonds autocorrelation using GROMACS
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0
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41
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August 11, 2026
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Use of the CRYST1 values in the DSSP calculation
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8
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113
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August 10, 2026
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[TOOL] GROMACS Trajectory Displayer — Web Dashboard for Trajectory Analysis & Visualization
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0
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35
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July 30, 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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78
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July 24, 2026
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How to remove duplicate frames
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2
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41
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July 20, 2026
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DNA and protein grouping for RMSD calculations
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0
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37
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July 17, 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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42
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July 10, 2026
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gmx_MMPBSA error in Steered Molecular dynamics simulation trajectory
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1
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50
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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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48
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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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71
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July 8, 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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57
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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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40
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June 24, 2026
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Run gmx energy on a large number of systems
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2
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46
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June 18, 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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80
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June 3, 2026
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Details of viscosity estimation (gmx energy -vis)
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6
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1360
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May 11, 2026
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"Segmentation fault", "std::bad_alloc" and "malloc(): invalid size" when running gmx hbond
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11
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1395
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April 30, 2026
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Would x3DNA/DSSR functionality built into Gromacs be useful?
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3
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80
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April 10, 2026
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Segmentation fault - pairdist
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1
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56
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April 7, 2026
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GMX Polystat MSID
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4
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63
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March 25, 2026
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How does "-[no]correct (no)" flag works in gmx potential tool?
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12
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485
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March 20, 2026
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Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
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6
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79
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March 15, 2026
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How to plot viscosity in xmgrace by gmx tcaf
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2
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34
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March 3, 2026
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Equilibration not work
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0
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36
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February 17, 2026
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Questions regarding AWH and comparison to MBAR
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3
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137
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February 10, 2026
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Free energy verification by thermodynamic integration in liquid solutions
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0
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70
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January 22, 2026
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The output average of gmx energy differs from the average of the data stored in .xvg
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3
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70
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January 22, 2026
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gmx_MMPBSA: a new tool aiming to perform end-state free energy calculations with GROMACS files
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2
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2333
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January 14, 2026
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Wrapping trajectories in trjconv
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5
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226
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December 15, 2025
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PCA and DCCA analysis
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1
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53
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December 6, 2025
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