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Help centering, fitting, and analysis on a protein that contains a chain of D-residues
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1
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21
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February 3, 2025
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RMSD value very high
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1
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23
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January 27, 2025
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Removing PBC for peptide-lipid system
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8
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1954
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November 3, 2024
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Gmx trjconv Index Error
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7
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55
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October 31, 2024
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Gromacs Hbdons
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0
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13
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September 18, 2024
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Error when converting files between gromacs 2019.6 and gromacs 5.1.5
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5
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25
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September 4, 2024
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Gmx covar: error due to the PBC
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18
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83
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August 28, 2024
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Jumping residue after PBC removal
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13
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256
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August 26, 2024
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Using pdb2gmx as a lib
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0
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16
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August 20, 2024
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Using frame numbers from index file for naming output files
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1
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74
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June 30, 2024
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Saving velocities and forces for a subset of the trajectory
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1
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80
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June 3, 2024
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Protein come out of the box but trjconv command didn't fix the problem
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9
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3835
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April 3, 2024
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Trajectory slicing changes 3D coordinates
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1
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156
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March 7, 2024
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Inquiry Regarding Differences in Protein Centering Behavior between Amber and GROMACS
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5
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239
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February 19, 2024
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Removal of one leaflet causing errors in trajectory
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3
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115
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February 14, 2024
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How to centralize membrane on Z = 0
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2
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274
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February 5, 2024
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Trjconv ignoring chainIDs (molblock) from TPR
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0
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122
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January 23, 2024
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RMSD calculation error
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1
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209
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December 6, 2023
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How to fix RMSD analysis results?
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7
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523
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November 5, 2023
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Problem for gmx trjconv
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1
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734
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October 11, 2023
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Error in recentering and rewrapping coordinates
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3
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331
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September 25, 2023
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Cannot make protein whole
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1
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310
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July 7, 2023
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Is PBC correction necessary for some particular type of analysis?
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2
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957
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May 30, 2023
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Error when using a bash loop
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1
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308
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May 19, 2023
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PBC correction during Umbrella sampling configuration generation
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2
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279
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May 19, 2023
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Trjconv not writing chain identifiers anymore (since ca. v2019)
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4
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422
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May 2, 2023
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Fit trajectories (trjconv) issue
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2
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1241
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March 15, 2023
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Trjconv -dt does not output frames at correct times
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0
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319
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March 2, 2023
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Gmx trjconv
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1
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589
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February 17, 2023
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Error in gmx do_dssp
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8
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1893
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December 11, 2022
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