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Centering a micelle in a gro file, but it's cut by box boundary
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1
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17
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July 28, 2025
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MMPBSA for custom atom types
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0
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16
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July 20, 2025
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Error in topology conversion from CGenFF
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0
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24
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July 1, 2025
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How to create restrained file for sol
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0
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12
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July 15, 2025
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Number of digits in rdf data
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0
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9
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July 14, 2025
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Hbond calculation
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3
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837
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July 14, 2025
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How to use gmx hbond to analyze hydrogen bond between two chains of a homodimer?
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4
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1072
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July 9, 2025
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gmx_clusterByFeatures - Features-based conformational clustering from MD Simulations
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0
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28
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July 7, 2025
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Gmx make_ndx - index Ca and H instead of N and H
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0
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16
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June 22, 2025
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AWH multiple .xvg files analysis
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1
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16
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June 5, 2025
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Unusual RMSD of ligand-protein
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6
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102
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May 23, 2025
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ERROR 1 [file dd.itp, line 198]: No default Proper Dih. types
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0
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22
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May 19, 2025
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Fatal error: Residue 175 named GLU of a molecule in the input file was mapped to an entry in the top
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0
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11
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May 18, 2025
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Atom C1 not found in building block 1MET while combining tbp and trp
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0
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54
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May 18, 2025
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Entropy calculation output
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3
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807
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May 16, 2025
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gorder: Comprehensive tool for calculating lipid order parameters from molecular simulations
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0
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29
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May 12, 2025
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Interpretation of Nonzero 14-LJ and 14-Coul Terms for Nonbonded Groups
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7
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42
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May 8, 2025
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listRanges does not have a first element with value 0
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3
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142
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April 12, 2025
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SMD output files and interpretation
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0
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12
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May 2, 2025
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The options about xmax and xmin for gmx densmap
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1
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29
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May 2, 2025
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Rotating protein in trajectory
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6
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47
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May 1, 2025
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Protein-Lipid system, protein keeps flipping or jumping
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2
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47
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April 25, 2025
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Is an RMSD value above 0.36 nm (apo-form) and 0.4 to 0.5 nm (complex-form) is acceptable?
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0
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18
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April 23, 2025
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Debye Method Implementation
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0
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25
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April 22, 2025
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Error in docked complex simulation
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1
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33
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April 22, 2025
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Equivalent to the old sas2mat
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0
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15
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April 17, 2025
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GROMACS Result Analysis. Potential Issues?
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7
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137
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April 17, 2025
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PBC Artifacts in 20 bp DNA System
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0
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7
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April 16, 2025
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Topology for janus MoSSe
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0
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7
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April 14, 2025
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For two examples, the eigenvalues obtained from `g_covar` are all zeros
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3
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42
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April 11, 2025
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