|
Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'complex.top'
|
|
2
|
13
|
November 29, 2025
|
|
Simulating a Reverse Transcriptase complex with RNA, DNA
|
|
0
|
5
|
November 28, 2025
|
|
Dimeric protein handling during simulation
|
|
1
|
21
|
November 27, 2025
|
|
INSANE not compatible with martini3 GM3?
|
|
0
|
17
|
November 27, 2025
|
|
RNA simulation error with phosphate group atoms of the first nucleotide
|
|
3
|
22
|
November 26, 2025
|
|
Box explodes using NPT.mdp
|
|
2
|
18
|
November 26, 2025
|
|
Query regarding making all .mdp files for ionization, equllibration, energy minimization
|
|
2
|
19
|
November 25, 2025
|
|
Query:Reagrding using the multiple nodes's GPU or CPU to run MD production step in gromacs
|
|
4
|
40
|
November 20, 2025
|
|
How to determine the number of water molecules in a box? gmx insert-molecules or gmx solvate?
|
|
8
|
71
|
November 20, 2025
|
|
Best practice for using newer AMBER force fields (ff19SB) in GROMACS?
|
|
2
|
75
|
November 19, 2025
|
|
Simulate the freezing of saline under an external electric field
|
|
12
|
73
|
November 13, 2025
|
|
Non-Bonded parameters definition not working
|
|
2
|
28
|
November 10, 2025
|
|
GROMACS number of molecules
|
|
0
|
14
|
November 8, 2025
|
|
Free-energy on virtual sites only (or vice versa)
|
|
2
|
49
|
October 29, 2025
|
|
How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
|
|
9
|
128
|
October 26, 2025
|
|
ZINK in Protein
|
|
4
|
61
|
October 21, 2025
|
|
Umbrella sampling PMFs with additional restraints
|
|
0
|
36
|
October 20, 2025
|
|
Water accumulation in slab geometry
|
|
0
|
25
|
October 20, 2025
|
|
A Custom Water Force Field Implementation
|
|
0
|
28
|
October 17, 2025
|
|
Modify residues using CHARMM-GUI pdb reader and manipulator
|
|
0
|
27
|
October 14, 2025
|
|
GROMACS 2025.3 CUDA 13 RTX 5070 Ti Fails on Simulations
|
|
2
|
49
|
October 14, 2025
|
|
Performance of SMD simulation
|
|
1
|
35
|
October 10, 2025
|
|
How to simulate a cyclic protein with AMBER99SB ff?
|
|
1
|
27
|
October 9, 2025
|
|
Tools for creating initial .gro and combining source files
|
|
0
|
17
|
October 8, 2025
|
|
what should do with zink-protein.pdf to get topology file?
|
|
5
|
46
|
October 7, 2025
|
|
Help: RTX 5080 (Blackwell, Compute Capability 12.1) + WSL2 + CUDA 13.0 “No Kernel Image Available”
|
|
2
|
149
|
October 5, 2025
|
|
Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
|
|
2
|
42
|
October 5, 2025
|
|
How should I choose the box size for nanodisc simulations?
|
|
1
|
29
|
October 3, 2025
|
|
Hydrogen bonds increase with temperature in MD simulation – unexpected behavior
|
|
4
|
67
|
October 3, 2025
|
|
x2top for MINFF
|
|
0
|
32
|
October 2, 2025
|