|
Ligand dissociation in certain frames when viewing in pymol
|
|
1
|
35
|
November 5, 2026
|
|
Ligand dissociation from the binding pocket and high RMSD (>8 Å) during a 200 ns MD simulation using
|
|
0
|
28
|
October 21, 2026
|
|
How create uneven box for all-atom simulation
|
|
4
|
71
|
October 15, 2026
|
|
DSSNA — nucleic acids secondary/tertiary structure analysis tool for MD trajectories
|
|
2
|
108
|
October 7, 2026
|
|
GROMACS hydrogen-bond analysis question
|
|
1
|
56
|
September 22, 2026
|
|
Having issue with gmx SASA giving values of 0 for specific protein
|
|
0
|
57
|
September 8, 2026
|
|
Running gmx_mmpbsa for protein receptor - homodimer protein complex
|
|
0
|
62
|
August 18, 2026
|
|
hbonds autocorrelation using GROMACS
|
|
0
|
93
|
August 11, 2026
|
|
Use of the CRYST1 values in the DSSP calculation
|
|
8
|
147
|
August 10, 2026
|
|
[TOOL] GROMACS Trajectory Displayer — Web Dashboard for Trajectory Analysis & Visualization
|
|
0
|
83
|
July 30, 2026
|
|
When is trajectory preprocessing (whole/cluster/nojump/center) actually required for analysis?
|
|
2
|
118
|
July 24, 2026
|
|
How to remove duplicate frames
|
|
2
|
66
|
July 20, 2026
|
|
DNA and protein grouping for RMSD calculations
|
|
0
|
51
|
July 17, 2026
|
|
PBC correction for ionisable lipid–lipid bilayer system (GROMACS 2025.4)
|
|
0
|
55
|
July 10, 2026
|
|
gmx_MMPBSA error in Steered Molecular dynamics simulation trajectory
|
|
1
|
65
|
July 9, 2026
|
|
G_mmpbsa for the gromacs 2025 versions
|
|
1
|
65
|
July 9, 2026
|
|
Atoms not completely removed by convert-tpr
|
|
3
|
99
|
July 8, 2026
|
|
Standard publishable preprocessing of AlphaFold3 complex structures for GROMACS MD simulations
|
|
0
|
71
|
June 24, 2026
|
|
Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding
|
|
1
|
47
|
June 24, 2026
|
|
Run gmx energy on a large number of systems
|
|
2
|
57
|
June 18, 2026
|
|
Gmx anaeig problematic error "Dimensions in the eigenvector files don't match"
|
|
4
|
99
|
June 3, 2026
|
|
Details of viscosity estimation (gmx energy -vis)
|
|
6
|
1425
|
May 11, 2026
|
|
"Segmentation fault", "std::bad_alloc" and "malloc(): invalid size" when running gmx hbond
|
|
11
|
1437
|
April 30, 2026
|
|
Would x3DNA/DSSR functionality built into Gromacs be useful?
|
|
3
|
102
|
April 10, 2026
|
|
Segmentation fault - pairdist
|
|
1
|
69
|
April 7, 2026
|
|
GMX Polystat MSID
|
|
4
|
72
|
March 25, 2026
|
|
How does "-[no]correct (no)" flag works in gmx potential tool?
|
|
12
|
611
|
March 20, 2026
|
|
Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
|
|
6
|
120
|
March 15, 2026
|
|
How to plot viscosity in xmgrace by gmx tcaf
|
|
2
|
37
|
March 3, 2026
|
|
Equilibration not work
|
|
0
|
38
|
February 17, 2026
|