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When is trajectory preprocessing (whole/cluster/nojump/center) actually required for analysis?
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2
|
45
|
July 24, 2026
|
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PBC wrapping for Protein-Ligand-Surface system
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0
|
19
|
July 7, 2026
|
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PBC effect on RMSD calculation
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2
|
103
|
October 1, 2025
|
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PBC correction for drug–lipid bilayer system (GROMACS 2024.5)
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0
|
70
|
August 19, 2025
|
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Error running Periodic graphene with mpi threads
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|
0
|
35
|
May 29, 2025
|
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PBC artifact issue
|
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0
|
69
|
April 12, 2025
|
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Issue with correcting PBC for DNA Separation in GROMACS
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7
|
163
|
January 15, 2025
|
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Handling of PBCs with multiple peptides
|
|
2
|
53
|
January 7, 2025
|
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Drift of the system in the periodic box during simulations
|
|
2
|
120
|
December 17, 2024
|
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System getting out of box upon simulation
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|
2
|
320
|
October 29, 2024
|
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Jumping residue after PBC removal
|
|
13
|
716
|
August 26, 2024
|
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Fix two separate DNA strands after simulation using -pbc cluster
|
|
0
|
54
|
July 22, 2024
|
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Manual Error Regarding Rhombic Dodecahedral Cell?
|
|
1
|
161
|
April 30, 2024
|
|
Trajectory slicing changes 3D coordinates
|
|
1
|
188
|
March 7, 2024
|
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Is PBC correction necessary for some particular type of analysis?
|
|
2
|
1179
|
May 30, 2023
|
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Unification of box shapes in molecular simulations
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|
2
|
563
|
March 16, 2023
|
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PBC correction doesn't remove all PBCs
|
|
0
|
694
|
November 2, 2022
|
|
Remove PBC effects on membrane+protein+ligand
|
|
4
|
673
|
October 20, 2022
|
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Making densities (multimers/aggregates/objects) whole over PBC
|
|
0
|
731
|
February 9, 2022
|
|
Why does molecules in MD trajectory go out of the pbc box in VMD / pymol?
|
|
1
|
1118
|
January 21, 2022
|
|
Pbc correction
|
|
1
|
472
|
November 12, 2021
|
|
Remove PBC
|
|
1
|
712
|
September 27, 2021
|
|
Starting simulation from another trajectory using -t grompp option - How are PBC treated?
|
|
3
|
771
|
March 30, 2021
|