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MSD curve has a large non-linear part
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5
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123
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March 26, 2025
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How to use gmx polystat for MSID
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3
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52
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March 26, 2025
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Distance between COM HP-beta-cyclodextrin and Gliclazide
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2
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52
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March 24, 2025
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Ligand leaving binding pocket
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15
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327
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March 23, 2025
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Can we calculate the MSD by considering only the first portion of the MSD graph?
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0
|
41
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March 21, 2025
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Increase in potential energy of peptide conformations Post MD run
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4
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49
|
March 18, 2025
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Head group atom of lipids
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4
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71
|
March 17, 2025
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In gmx wham, what is profile.xvg?
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0
|
47
|
March 11, 2025
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Change in position of Histidine residue lead to difference in columb interaction energy
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0
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17
|
March 3, 2025
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How gmx RMS read the input of group selection
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1
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43
|
March 1, 2025
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Failed to run long trajectory to compute MSD
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0
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24
|
February 27, 2025
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How to calculate Pairwise RMSD between two trajectories using `gmx rms`
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1
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133
|
February 22, 2025
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Very high solvation free energy value
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1
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66
|
February 19, 2025
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Gmx sasa for single atom in protein
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0
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45
|
February 19, 2025
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Free energy difference is zero for non-zero coulomb-lambdas during solvation free energy calculation
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3
|
63
|
February 13, 2025
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RMSD Analysis for POPC Membrane
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|
1
|
73
|
February 12, 2025
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RMSD Analysis for Protein-ligand-POPC Membrane System
|
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0
|
55
|
February 11, 2025
|
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H-bond calculations
|
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0
|
75
|
February 7, 2025
|
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CpHMD Simulation Analysis
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|
1
|
80
|
February 7, 2025
|
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WHAM of SMD doesn't generate a complete curve
|
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0
|
50
|
February 4, 2025
|
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Understanding RMSD and radius of gyration for an Intrinsically Disordered 30-Residue Peptide
|
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2
|
200
|
February 4, 2025
|
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Solvation free energy calculation of organic molecule in binary mixtures and convergence
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3
|
90
|
January 29, 2025
|
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Pbc mol with center not working
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0
|
25
|
February 3, 2025
|
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Help centering, fitting, and analysis on a protein that contains a chain of D-residues
|
|
1
|
61
|
February 3, 2025
|
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How to select amide hydrogen in a cyclic peptide nanotube in index file?
|
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0
|
31
|
February 2, 2025
|
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High Fluctuations in DNA RMSD Analysis After PBC Correction
|
|
6
|
156
|
January 30, 2025
|
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How to calculate long-range interactions using GROMACS?
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3
|
79
|
January 28, 2025
|
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RMSD value very high
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1
|
75
|
January 27, 2025
|
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Getting very high RMSD value after 75ns
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4
|
137
|
January 24, 2025
|
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Issue while extracting pdb from trajectory
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|
2
|
98
|
January 22, 2025
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