|
Membrane Protein ligand simulation
|
|
9
|
188
|
July 7, 2025
|
|
Restraining Solvent Molecules Under an Ice Slab
|
|
0
|
12
|
July 6, 2025
|
|
Segmentration Fault and to small of a timestep problem from a Amber built system
|
|
19
|
547
|
November 11, 2024
|
|
How to simulate the specific residues by mentioning their position in the sequence?
|
|
0
|
14
|
July 3, 2025
|
|
74% GPU utilization and 2/3 power usage on WSL2
|
|
1
|
26
|
July 2, 2025
|
|
Simulation with a 3 fs timestep
|
|
0
|
23
|
June 30, 2025
|
|
During Energy minimization error "Listed nonbonded interaction between particles 4778 and 4797 at d"
|
|
1
|
15
|
June 28, 2025
|
|
Using -membed option in gromacs
|
|
0
|
24
|
June 25, 2025
|
|
LINCS Warning or Freeze Behavior Depends on GROMACS Version
|
|
0
|
15
|
June 20, 2025
|
|
Unexpected geometry change when combing `freezegrps` with `constraints` and running MD
|
|
6
|
33
|
June 19, 2025
|
|
Membrane protein simulation
|
|
1
|
22
|
June 18, 2025
|
|
GROMACS cant detect GPU (AMD)
|
|
7
|
126
|
May 27, 2025
|
|
Unusual RMSD of ligand-protein
|
|
6
|
92
|
May 23, 2025
|
|
Mdrun crashes with some md parameter during NPT (gmx compiled for rocm,AdaptiveCPP)
|
|
8
|
72
|
May 22, 2025
|
|
Error While running npt equillibration of last frames extracted form complex
|
|
0
|
14
|
May 22, 2025
|
|
System has non-zero total charge: -1.000000
|
|
1
|
24
|
May 19, 2025
|
|
ERROR 1 [file dd.itp, line 198]: No default Proper Dih. types
|
|
0
|
19
|
May 19, 2025
|
|
Error ABFE calculation
|
|
0
|
17
|
May 19, 2025
|
|
Splitting 100ns Gromacs runs into 25ns smaller chunks
|
|
0
|
32
|
May 19, 2025
|
|
RESNAME error while using cgenff_charmm2gmx script
|
|
1
|
237
|
May 18, 2025
|
|
MSD changes with .xtc timestep
|
|
0
|
22
|
May 17, 2025
|
|
Segmentation fault or cuda error #700 during eABF/WTM-eABF calculations
|
|
0
|
9
|
May 17, 2025
|
|
Ligand Preparation for CHARMM36ff - Issue with halogens (Cl, Br)
|
|
0
|
22
|
May 13, 2025
|
|
Rerun xtc file generates different potential energies compared to original data
|
|
2
|
24
|
May 14, 2025
|
|
Need help minimising a backmapped system (I used backward method)
|
|
0
|
13
|
May 12, 2025
|
|
Update Groups Can't Be Created for GROMACS2024
|
|
2
|
37
|
May 6, 2025
|
|
Fixing coordinates of a chain after simulation
|
|
6
|
48
|
May 4, 2025
|
|
SMD output files and interpretation
|
|
0
|
11
|
May 2, 2025
|
|
RTX 5070 Not Utilized
|
|
2
|
175
|
April 30, 2025
|
|
How do we omit the positive/negative strain at zero stress?
|
|
1
|
29
|
April 29, 2025
|