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Create .xtc file with rectangular unit cell?
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7
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76
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November 14, 2025
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Bad diagrams for a protein complex, maybe because of bad trjconv
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6
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101
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October 12, 2025
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PBC effect on RMSD calculation
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2
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43
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October 1, 2025
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Energy minimizing multiple frames of an MD trajectory
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0
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24
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September 12, 2025
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Protein come out of the box but trjconv command didn't fix the problem
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10
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4437
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August 2, 2025
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Making a trajectory by listing frames
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1
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22
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May 28, 2025
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Issue: Unable to Remove PBC in GROMACS Using trjconv Options
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1
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115
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March 24, 2025
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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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64
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February 3, 2025
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RMSD value very high
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1
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83
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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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2109
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November 3, 2024
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Gmx trjconv Index Error
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7
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168
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October 31, 2024
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Gromacs Hbdons
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0
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19
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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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74
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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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222
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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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601
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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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20
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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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96
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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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130
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June 3, 2024
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Trajectory slicing changes 3D coordinates
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1
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174
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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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293
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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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137
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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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396
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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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134
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January 23, 2024
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RMSD calculation error
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1
|
240
|
December 6, 2023
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How to fix RMSD analysis results?
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7
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619
|
November 5, 2023
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Problem for gmx trjconv
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1
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834
|
October 11, 2023
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Error in recentering and rewrapping coordinates
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3
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402
|
September 25, 2023
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Cannot make protein whole
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1
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361
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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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1106
|
May 30, 2023
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Error when using a bash loop
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1
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317
|
May 19, 2023
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