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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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119
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July 24, 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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55
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July 10, 2026
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Create .xtc file with rectangular unit cell?
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7
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180
|
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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157
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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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170
|
October 1, 2025
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Energy minimizing multiple frames of an MD trajectory
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0
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51
|
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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4731
|
August 2, 2025
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Making a trajectory by listing frames
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1
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56
|
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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195
|
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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105
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February 3, 2025
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RMSD value very high
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1
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164
|
January 27, 2025
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Removing PBC for peptide-lipid system
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8
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2292
|
November 3, 2024
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Gmx trjconv Index Error
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7
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316
|
October 31, 2024
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Gromacs Hbdons
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0
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34
|
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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143
|
September 4, 2024
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Gmx covar: error due to the PBC
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18
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502
|
August 28, 2024
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Jumping residue after PBC removal
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13
|
823
|
August 26, 2024
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Using pdb2gmx as a lib
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0
|
30
|
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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147
|
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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169
|
June 3, 2024
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Trajectory slicing changes 3D coordinates
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1
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197
|
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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344
|
February 19, 2024
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Removal of one leaflet causing errors in trajectory
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3
|
177
|
February 14, 2024
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How to centralize membrane on Z = 0
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2
|
464
|
February 5, 2024
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Trjconv ignoring chainIDs (molblock) from TPR
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0
|
152
|
January 23, 2024
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RMSD calculation error
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|
1
|
270
|
December 6, 2023
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How to fix RMSD analysis results?
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7
|
713
|
November 5, 2023
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Problem for gmx trjconv
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1
|
908
|
October 11, 2023
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Error in recentering and rewrapping coordinates
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3
|
474
|
September 25, 2023
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Cannot make protein whole
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1
|
397
|
July 7, 2023
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