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The contradiction between the mdp settings and the real pull rate
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13
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41
|
February 4, 2026
|
|
Simulated annealing of protein-DNA complex
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0
|
34
|
February 3, 2026
|
|
SAM co-factor with CHARMM force field for GROMACS silmualtion
|
|
10
|
258
|
February 3, 2026
|
|
Gmx filter
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26
|
249
|
February 2, 2026
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Why not protein is not come in the selection
|
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1
|
10
|
January 31, 2026
|
|
Question about how LINCS calculates stress
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5
|
51
|
January 30, 2026
|
|
Umbrella sampling for a protien ligand system
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1
|
32
|
January 29, 2026
|
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Error problem
|
|
1
|
21
|
January 29, 2026
|
|
Absolute FEP result too high
|
|
2
|
35
|
January 29, 2026
|
|
MPI error when using ensemble-averaged distance restraints and set GMX_DISRE_ENSEMBLE_SIZE
|
|
10
|
68
|
January 27, 2026
|
|
Is is good to simulate lipid bilayer with NVE ensemble
|
|
0
|
24
|
January 26, 2026
|
|
Pdb2gmx handling altlocs
|
|
1
|
18
|
January 26, 2026
|
|
Struggling to replicate free energy calculations in pmx tutorial using FEP
|
|
0
|
42
|
January 26, 2026
|
|
How to add hydrogen atoms to the complex with correct coordinates?
|
|
2
|
23
|
January 23, 2026
|
|
Free energy verification by thermodynamic integration in liquid solutions
|
|
0
|
20
|
January 22, 2026
|
|
Segmentation faults / ‘core dumped’ errors
|
|
12
|
74
|
January 22, 2026
|
|
The output average of gmx energy differs from the average of the data stored in .xvg
|
|
3
|
15
|
January 22, 2026
|
|
DSSP stuck
|
|
0
|
12
|
January 22, 2026
|
|
Tabulated nonbonded potentials in GROMACS 2026
|
|
1
|
34
|
January 21, 2026
|
|
Pdb2gmx rounds up the charge of a single atom
|
|
7
|
41
|
January 21, 2026
|
|
Charge precision in topology files: parsing behaviour and validation tolerance
|
|
5
|
48
|
January 21, 2026
|
|
Comparing Simulations with Different Thermo/Barostats
|
|
2
|
48
|
January 21, 2026
|
|
Water box elongation
|
|
1
|
26
|
January 21, 2026
|
|
Post MD simulation Visualizations
|
|
2
|
68
|
January 15, 2026
|
|
Gromacs .hdb format RU5 case study
|
|
3
|
25
|
January 14, 2026
|
|
Slow simulation
|
|
3
|
56
|
January 12, 2026
|
|
Npt vs nvt
|
|
1
|
40
|
January 11, 2026
|
|
COF molecular dynamics simulation model creation
|
|
1
|
75
|
January 10, 2026
|
|
All atom membrane
|
|
0
|
28
|
January 9, 2026
|
|
Protein ns MD simulation and other times recommended inquiry?
|
|
21
|
497
|
January 8, 2026
|