|
Steered MD Simulation using Gromacs
|
|
2
|
29
|
January 7, 2026
|
|
High pressure in x and y axis in a buble in a nano channel
|
|
2
|
19
|
January 5, 2026
|
|
Should I manually set -ntomp 16 or let Gromacs auto-configure its settings？
|
|
4
|
48
|
December 29, 2025
|
|
Best practice for using newer AMBER force fields (ff19SB) in GROMACS?
|
|
3
|
191
|
December 17, 2025
|
|
Steered molecular dynamics - umbrella samling
|
|
1
|
34
|
December 8, 2025
|
|
How to add terminal caps in AMBER with GROMACS
|
|
1
|
40
|
December 3, 2025
|
|
INSANE not compatible with martini3 GM3?
|
|
1
|
37
|
December 1, 2025
|
|
Simulating a Reverse Transcriptase complex with RNA, DNA
|
|
1
|
18
|
December 1, 2025
|
|
Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'complex.top'
|
|
2
|
29
|
November 29, 2025
|
|
Dimeric protein handling during simulation
|
|
1
|
28
|
November 27, 2025
|
|
RNA simulation error with phosphate group atoms of the first nucleotide
|
|
3
|
26
|
November 26, 2025
|
|
Box explodes using NPT.mdp
|
|
2
|
47
|
November 26, 2025
|
|
Query regarding making all .mdp files for ionization, equllibration, energy minimization
|
|
2
|
35
|
November 25, 2025
|
|
Query:Reagrding using the multiple nodes's GPU or CPU to run MD production step in gromacs
|
|
4
|
53
|
November 20, 2025
|
|
How to determine the number of water molecules in a box? gmx insert-molecules or gmx solvate?
|
|
8
|
95
|
November 20, 2025
|
|
Simulate the freezing of saline under an external electric field
|
|
12
|
124
|
November 13, 2025
|
|
Non-Bonded parameters definition not working
|
|
2
|
35
|
November 10, 2025
|
|
GROMACS number of molecules
|
|
0
|
16
|
November 8, 2025
|
|
Free-energy on virtual sites only (or vice versa)
|
|
2
|
59
|
October 29, 2025
|
|
How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
|
|
9
|
217
|
October 26, 2025
|
|
ZINK in Protein
|
|
4
|
75
|
October 21, 2025
|
|
Umbrella sampling PMFs with additional restraints
|
|
0
|
49
|
October 20, 2025
|
|
Water accumulation in slab geometry
|
|
0
|
30
|
October 20, 2025
|
|
A Custom Water Force Field Implementation
|
|
0
|
32
|
October 17, 2025
|
|
Modify residues using CHARMM-GUI pdb reader and manipulator
|
|
0
|
34
|
October 14, 2025
|
|
GROMACS 2025.3 CUDA 13 RTX 5070 Ti Fails on Simulations
|
|
2
|
76
|
October 14, 2025
|
|
Performance of SMD simulation
|
|
1
|
40
|
October 10, 2025
|
|
How to simulate a cyclic protein with AMBER99SB ff?
|
|
1
|
39
|
October 9, 2025
|
|
Tools for creating initial .gro and combining source files
|
|
0
|
19
|
October 8, 2025
|
|
what should do with zink-protein.pdf to get topology file?
|
|
5
|
50
|
October 7, 2025
|