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PBCs in a slightly complex system
|
|
7
|
146
|
September 15, 2026
|
|
When is trajectory preprocessing (whole/cluster/nojump/center) actually required for analysis?
|
|
2
|
118
|
July 24, 2026
|
|
PBC wrapping for Protein-Ligand-Surface system
|
|
0
|
33
|
July 7, 2026
|
|
PBC effect on RMSD calculation
|
|
2
|
169
|
October 1, 2025
|
|
PBC correction for drug–lipid bilayer system (GROMACS 2024.5)
|
|
0
|
80
|
August 19, 2025
|
|
Error running Periodic graphene with mpi threads
|
|
0
|
44
|
May 29, 2025
|
|
PBC artifact issue
|
|
0
|
85
|
April 12, 2025
|
|
Issue with correcting PBC for DNA Separation in GROMACS
|
|
7
|
214
|
January 15, 2025
|
|
Handling of PBCs with multiple peptides
|
|
2
|
60
|
January 7, 2025
|
|
Drift of the system in the periodic box during simulations
|
|
2
|
138
|
December 17, 2024
|
|
System getting out of box upon simulation
|
|
2
|
345
|
October 29, 2024
|
|
Jumping residue after PBC removal
|
|
13
|
822
|
August 26, 2024
|
|
Fix two separate DNA strands after simulation using -pbc cluster
|
|
0
|
68
|
July 22, 2024
|
|
Manual Error Regarding Rhombic Dodecahedral Cell?
|
|
1
|
168
|
April 30, 2024
|
|
Trajectory slicing changes 3D coordinates
|
|
1
|
197
|
March 7, 2024
|
|
Is PBC correction necessary for some particular type of analysis?
|
|
2
|
1238
|
May 30, 2023
|
|
Unification of box shapes in molecular simulations
|
|
2
|
576
|
March 16, 2023
|
|
PBC correction doesn't remove all PBCs
|
|
0
|
706
|
November 2, 2022
|
|
Remove PBC effects on membrane+protein+ligand
|
|
4
|
704
|
October 20, 2022
|
|
Making densities (multimers/aggregates/objects) whole over PBC
|
|
0
|
743
|
February 9, 2022
|
|
Why does molecules in MD trajectory go out of the pbc box in VMD / pymol?
|
|
1
|
1134
|
January 21, 2022
|
|
Pbc correction
|
|
1
|
479
|
November 12, 2021
|
|
Remove PBC
|
|
1
|
725
|
September 27, 2021
|
|
Starting simulation from another trajectory using -t grompp option - How are PBC treated?
|
|
3
|
785
|
March 30, 2021
|