|
Standard publishable preprocessing of AlphaFold3 complex structures for GROMACS MD simulations
|
|
0
|
39
|
June 24, 2026
|
|
Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding
|
|
1
|
26
|
June 24, 2026
|
|
gmx_MMPBSA error in Steered Molecular dynamics simulation trajectory
|
|
0
|
24
|
June 21, 2026
|
|
Run gmx energy on a large number of systems
|
|
2
|
37
|
June 18, 2026
|
|
Atoms not completely removed by convert-tpr
|
|
2
|
40
|
June 15, 2026
|
|
Gmx anaeig problematic error "Dimensions in the eigenvector files don't match"
|
|
4
|
48
|
June 3, 2026
|
|
Details of viscosity estimation (gmx energy -vis)
|
|
6
|
1279
|
May 11, 2026
|
|
"Segmentation fault", "std::bad_alloc" and "malloc(): invalid size" when running gmx hbond
|
|
11
|
1316
|
April 30, 2026
|
|
Would x3DNA/DSSR functionality built into Gromacs be useful?
|
|
3
|
70
|
April 10, 2026
|
|
Segmentation fault - pairdist
|
|
1
|
50
|
April 7, 2026
|
|
GMX Polystat MSID
|
|
4
|
48
|
March 25, 2026
|
|
How does "-[no]correct (no)" flag works in gmx potential tool?
|
|
12
|
343
|
March 20, 2026
|
|
Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
|
|
6
|
59
|
March 15, 2026
|
|
How to plot viscosity in xmgrace by gmx tcaf
|
|
2
|
27
|
March 3, 2026
|
|
Equilibration not work
|
|
0
|
33
|
February 17, 2026
|
|
Questions regarding AWH and comparison to MBAR
|
|
3
|
109
|
February 10, 2026
|
|
Free energy verification by thermodynamic integration in liquid solutions
|
|
0
|
45
|
January 22, 2026
|
|
The output average of gmx energy differs from the average of the data stored in .xvg
|
|
3
|
50
|
January 22, 2026
|
|
gmx_MMPBSA: a new tool aiming to perform end-state free energy calculations with GROMACS files
|
|
2
|
2266
|
January 14, 2026
|
|
Wrapping trajectories in trjconv
|
|
5
|
193
|
December 15, 2025
|
|
PCA and DCCA analysis
|
|
1
|
39
|
December 6, 2025
|
|
PCA and DCCA analysis
|
|
0
|
31
|
December 4, 2025
|
|
How to compute the number of hydrogen bonds per molecule in a pure water system: gmx hbond
|
|
1
|
287
|
December 3, 2025
|
|
How do we use gmx polystat?
|
|
4
|
359
|
December 2, 2025
|
|
Gmx chi Alanine residues output
|
|
1
|
46
|
November 30, 2025
|
|
Error in gmx hbond for parameter -hbm
|
|
2
|
66
|
November 26, 2025
|
|
Gmx Clustsize Error
|
|
2
|
507
|
November 20, 2025
|
|
How to make index group for backbone atoms of a protein chain
|
|
3
|
140
|
October 30, 2025
|
|
Change in Volume Fluctuations / Compressibility for TIP4P/2005 Between GROMACS 2016 and 2024
|
|
6
|
108
|
October 16, 2025
|
|
Gromacs DSSP Secondary structure analysis
|
|
1
|
180
|
October 15, 2025
|