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DNA and protein grouping for RMSD calculations
|
|
0
|
40
|
July 17, 2026
|
|
Issue with ligand preparation in CGENFF
|
|
0
|
35
|
July 15, 2026
|
|
Multiple gmx processes on GPU(s) ran too slowly
|
|
10
|
188
|
July 13, 2026
|
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Simulation of whole yeast ribosome to study single residue substitution in core RP
|
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0
|
25
|
July 13, 2026
|
|
RMSD for Protein-Ligand complex
|
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2
|
958
|
July 13, 2026
|
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Trajectory preprocessing in peptide self-assembly simulations
|
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0
|
36
|
July 12, 2026
|
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gmx_MMPBSA for big molecule
|
|
1
|
61
|
July 10, 2026
|
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PBC correction for ionisable lipid–lipid bilayer system (GROMACS 2025.4)
|
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0
|
42
|
July 10, 2026
|
|
GROMACS Courtesy
|
|
0
|
45
|
July 10, 2026
|
|
TIP4P/Ice .itp File
|
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0
|
33
|
July 9, 2026
|
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gmx_MMPBSA error in Steered Molecular dynamics simulation trajectory
|
|
1
|
54
|
July 9, 2026
|
|
G_mmpbsa for the gromacs 2025 versions
|
|
1
|
50
|
July 9, 2026
|
|
Atoms not completely removed by convert-tpr
|
|
3
|
72
|
July 8, 2026
|
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PBC wrapping for Protein-Ligand-Surface system
|
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0
|
27
|
July 7, 2026
|
|
Use of refcoordscaling in CHARMM and MARTINI
|
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0
|
25
|
July 7, 2026
|
|
Workstation options
|
|
2
|
124
|
July 7, 2026
|
|
Can CGenFF-generated partial charges differ significantly from QM-derived CHELPG (ESP) charges?
|
|
2
|
93
|
July 5, 2026
|
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RMSD analysis of the Protein-Ligand simulation
|
|
0
|
49
|
July 5, 2026
|
|
How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction
|
|
1
|
80
|
July 4, 2026
|
|
How to deal with Zn ion in Zinc finger protein
|
|
3
|
97
|
July 3, 2026
|
|
GROMACS 2026.2 duplicate type-9 dihedral errors with CHARMM36-feb2026 and CGenFF 5.0
|
|
1
|
45
|
July 3, 2026
|
|
How to determine b0 and kb in Zn-coordinated bond
|
|
0
|
37
|
July 2, 2026
|
|
How to generate a MOL2 ligand file with the correct docking pose, full hydrogens, and physiological
|
|
1
|
77
|
July 1, 2026
|
|
Efficient Workflow for Multiple Modified Residues
|
|
2
|
52
|
July 1, 2026
|
|
Ligand jumping around during GROMACS MD simulation after CHARMM-GUI setup – PBC issue or system prep
|
|
1
|
35
|
June 26, 2026
|
|
Gromacs 2025.4 + Plumed 2.10 Installation issue
|
|
0
|
45
|
June 26, 2026
|
|
Trying to perturb a torsion with multiple terms
|
|
1
|
31
|
June 25, 2026
|
|
Protein small molecule simulation
|
|
3
|
78
|
June 25, 2026
|
|
Temperature coupling
|
|
3
|
98
|
June 24, 2026
|
|
Standard publishable preprocessing of AlphaFold3 complex structures for GROMACS MD simulations
|
|
0
|
59
|
June 24, 2026
|