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Bad diagrams for a protein complex, maybe because of bad trjconv
|
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6
|
67
|
October 12, 2025
|
|
PBC effect on RMSD calculation
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|
2
|
12
|
October 1, 2025
|
|
Energy minimizing multiple frames of an MD trajectory
|
|
0
|
16
|
September 12, 2025
|
|
Protein come out of the box but trjconv command didn't fix the problem
|
|
10
|
4243
|
August 2, 2025
|
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Making a trajectory by listing frames
|
|
1
|
11
|
May 28, 2025
|
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Issue: Unable to Remove PBC in GROMACS Using trjconv Options
|
|
1
|
65
|
March 24, 2025
|
|
Help centering, fitting, and analysis on a protein that contains a chain of D-residues
|
|
1
|
42
|
February 3, 2025
|
|
RMSD value very high
|
|
1
|
63
|
January 27, 2025
|
|
Removing PBC for peptide-lipid system
|
|
8
|
2038
|
November 3, 2024
|
|
Gmx trjconv Index Error
|
|
7
|
121
|
October 31, 2024
|
|
Gromacs Hbdons
|
|
0
|
16
|
September 18, 2024
|
|
Error when converting files between gromacs 2019.6 and gromacs 5.1.5
|
|
5
|
43
|
September 4, 2024
|
|
Gmx covar: error due to the PBC
|
|
18
|
139
|
August 28, 2024
|
|
Jumping residue after PBC removal
|
|
13
|
454
|
August 26, 2024
|
|
Using pdb2gmx as a lib
|
|
0
|
18
|
August 20, 2024
|
|
Using frame numbers from index file for naming output files
|
|
1
|
83
|
June 30, 2024
|
|
Saving velocities and forces for a subset of the trajectory
|
|
1
|
107
|
June 3, 2024
|
|
Trajectory slicing changes 3D coordinates
|
|
1
|
158
|
March 7, 2024
|
|
Inquiry Regarding Differences in Protein Centering Behavior between Amber and GROMACS
|
|
5
|
272
|
February 19, 2024
|
|
Removal of one leaflet causing errors in trajectory
|
|
3
|
123
|
February 14, 2024
|
|
How to centralize membrane on Z = 0
|
|
2
|
355
|
February 5, 2024
|
|
Trjconv ignoring chainIDs (molblock) from TPR
|
|
0
|
126
|
January 23, 2024
|
|
RMSD calculation error
|
|
1
|
232
|
December 6, 2023
|
|
How to fix RMSD analysis results?
|
|
7
|
592
|
November 5, 2023
|
|
Problem for gmx trjconv
|
|
1
|
801
|
October 11, 2023
|
|
Error in recentering and rewrapping coordinates
|
|
3
|
373
|
September 25, 2023
|
|
Cannot make protein whole
|
|
1
|
330
|
July 7, 2023
|
|
Is PBC correction necessary for some particular type of analysis?
|
|
2
|
1056
|
May 30, 2023
|
|
Error when using a bash loop
|
|
1
|
312
|
May 19, 2023
|
|
PBC correction during Umbrella sampling configuration generation
|
|
2
|
297
|
May 19, 2023
|