|
Correct protocol for generating independent replicas of a membrane-protein simulation.
|
|
3
|
106
|
July 30, 2026
|
|
Advice on CGenFF penalty scores for a large, DFT-optimised molecule
|
|
4
|
123
|
July 29, 2026
|
|
Preprocessing error with CGenFF 5.0 topology: unsupported multiple CHARMM type-9 dihedral parameters
|
|
0
|
27
|
July 29, 2026
|
|
How create Charmm36 topology parameters for glycans
|
|
2
|
78
|
July 28, 2026
|
|
Parametrization of pyroglutamate
|
|
2
|
73
|
July 28, 2026
|
|
AWH convergence for a charged ligand permeating a bilayer
|
|
5
|
98
|
July 28, 2026
|
|
Trans to cis confirmation at NVT step
|
|
0
|
33
|
July 28, 2026
|
|
Regressiontests/complex tests fail with intelmpi GHROMACS build
|
|
1
|
57
|
July 27, 2026
|
|
How to simulate EDLC (Electrochemical Double Layer)?
|
|
1
|
172
|
July 24, 2026
|
|
Simulation of a dizinc metallo protein
|
|
6
|
606
|
July 24, 2026
|
|
When is trajectory preprocessing (whole/cluster/nojump/center) actually required for analysis?
|
|
2
|
106
|
July 24, 2026
|
|
Umbrella sampling simulation pulling towards periodic box using martini 3 forcefield
|
|
3
|
67
|
July 23, 2026
|
|
X2top not generating listed interactions correctly
|
|
1
|
55
|
July 23, 2026
|
|
Simulating an Infinite polymer across boundaries
|
|
1
|
59
|
July 23, 2026
|
|
"No default Per. Imp. Dih. types" when using amber14sb_parmbsc1_cufix force field
|
|
0
|
36
|
July 21, 2026
|
|
How to remove duplicate frames
|
|
2
|
47
|
July 20, 2026
|
|
Gmx order for unsaturated AII-Atom lipid chains
|
|
3
|
426
|
July 18, 2026
|
|
DNA and protein grouping for RMSD calculations
|
|
0
|
43
|
July 17, 2026
|
|
Issue with ligand preparation in CGENFF
|
|
0
|
44
|
July 15, 2026
|
|
Multiple gmx processes on GPU(s) ran too slowly
|
|
10
|
220
|
July 13, 2026
|
|
Simulation of whole yeast ribosome to study single residue substitution in core RP
|
|
0
|
27
|
July 13, 2026
|
|
RMSD for Protein-Ligand complex
|
|
2
|
997
|
July 13, 2026
|
|
Trajectory preprocessing in peptide self-assembly simulations
|
|
0
|
40
|
July 12, 2026
|
|
gmx_MMPBSA for big molecule
|
|
1
|
72
|
July 10, 2026
|
|
PBC correction for ionisable lipid–lipid bilayer system (GROMACS 2025.4)
|
|
0
|
48
|
July 10, 2026
|
|
GROMACS Courtesy
|
|
0
|
45
|
July 10, 2026
|
|
TIP4P/Ice .itp File
|
|
0
|
35
|
July 9, 2026
|
|
gmx_MMPBSA error in Steered Molecular dynamics simulation trajectory
|
|
1
|
63
|
July 9, 2026
|
|
G_mmpbsa for the gromacs 2025 versions
|
|
1
|
56
|
July 9, 2026
|
|
Atoms not completely removed by convert-tpr
|
|
3
|
92
|
July 8, 2026
|