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Energy minimizing multiple frames of an MD trajectory
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0
|
11
|
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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4200
|
August 2, 2025
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Making a trajectory by listing frames
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1
|
10
|
May 28, 2025
|
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Issue: Unable to Remove PBC in GROMACS Using trjconv Options
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1
|
61
|
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
|
41
|
February 3, 2025
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RMSD value very high
|
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1
|
62
|
January 27, 2025
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Removing PBC for peptide-lipid system
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8
|
2028
|
November 3, 2024
|
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Gmx trjconv Index Error
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7
|
109
|
October 31, 2024
|
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Gromacs Hbdons
|
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0
|
16
|
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
|
43
|
September 4, 2024
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Gmx covar: error due to the PBC
|
|
18
|
127
|
August 28, 2024
|
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Jumping residue after PBC removal
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|
13
|
418
|
August 26, 2024
|
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Using pdb2gmx as a lib
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0
|
17
|
August 20, 2024
|
|
Using frame numbers from index file for naming output files
|
|
1
|
83
|
June 30, 2024
|
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Saving velocities and forces for a subset of the trajectory
|
|
1
|
99
|
June 3, 2024
|
|
Trajectory slicing changes 3D coordinates
|
|
1
|
158
|
March 7, 2024
|
|
Inquiry Regarding Differences in Protein Centering Behavior between Amber and GROMACS
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5
|
268
|
February 19, 2024
|
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Removal of one leaflet causing errors in trajectory
|
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3
|
123
|
February 14, 2024
|
|
How to centralize membrane on Z = 0
|
|
2
|
341
|
February 5, 2024
|
|
Trjconv ignoring chainIDs (molblock) from TPR
|
|
0
|
126
|
January 23, 2024
|
|
RMSD calculation error
|
|
1
|
231
|
December 6, 2023
|
|
How to fix RMSD analysis results?
|
|
7
|
587
|
November 5, 2023
|
|
Problem for gmx trjconv
|
|
1
|
792
|
October 11, 2023
|
|
Error in recentering and rewrapping coordinates
|
|
3
|
371
|
September 25, 2023
|
|
Cannot make protein whole
|
|
1
|
329
|
July 7, 2023
|
|
Is PBC correction necessary for some particular type of analysis?
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|
2
|
1041
|
May 30, 2023
|
|
Error when using a bash loop
|
|
1
|
312
|
May 19, 2023
|
|
PBC correction during Umbrella sampling configuration generation
|
|
2
|
295
|
May 19, 2023
|
|
Trjconv not writing chain identifiers anymore (since ca. v2019)
|
|
4
|
455
|
May 2, 2023
|
|
Fit trajectories (trjconv) issue
|
|
2
|
1270
|
March 15, 2023
|