|
what should do with zink-protein.pdf to get topology file?
|
|
5
|
35
|
October 7, 2025
|
|
Inaccurate thermostatting when simulating MD water
|
|
1
|
24
|
October 4, 2025
|
|
Applying no cut off can affect the result?
|
|
1
|
26
|
September 23, 2025
|
|
Pressure scaling more than 1%. This may mean your system is not yet equilibrated
|
|
5
|
59
|
September 15, 2025
|
|
Energy minimization with position restraints in charmm-gui mdp file
|
|
5
|
1215
|
September 13, 2025
|
|
Comm-mode setting in applied field simulation in membrane-protein complex
|
|
3
|
41
|
September 9, 2025
|
|
RMSD graph after protein protein md simulation
|
|
4
|
66
|
September 8, 2025
|
|
Membrane artefacts when pulling membrane proteins together using Martini forcefield
|
|
3
|
23
|
September 4, 2025
|
|
Assistance Needed: "Atomtype F not found" Error in GROMACS Minimization with TFE Solvent
|
|
1
|
15
|
September 3, 2025
|
|
Unexplained calculation stalling during density fit
|
|
2
|
30
|
August 25, 2025
|
|
Pressure decreasing after npt equilibration
|
|
2
|
40
|
August 14, 2025
|
|
Maxwell distribution gen_t
|
|
6
|
42
|
August 12, 2025
|
|
Mdrun log file error Large VCM(group MEMB)
|
|
1
|
22
|
August 11, 2025
|
|
Osmotic pressure simulations using the pull code
|
|
6
|
64
|
August 7, 2025
|
|
Value too high for SFE (charmm-gui files)
|
|
5
|
40
|
August 6, 2025
|
|
Minimization of a membrane-peptide complex
|
|
0
|
19
|
August 2, 2025
|
|
How to read in an xyz vector from the .mdp file
|
|
1
|
41
|
July 28, 2025
|
|
Pressure Scaling more than 1% and volume fluctuations
|
|
1
|
56
|
July 25, 2025
|
|
Issues when equilibrating a membrane system with 2024.4 (not present in 2023.3)
|
|
1
|
28
|
July 22, 2025
|
|
Gen_vel=no and continuation=false
|
|
3
|
191
|
July 22, 2025
|
|
Homocysteine covalently bonded with a protein MD simulation how to perform
|
|
0
|
33
|
July 21, 2025
|
|
Computational Electrophysiology Setup with GROMACS (.mdp file)
|
|
3
|
254
|
July 19, 2025
|
|
Frozen beads - no movements
|
|
2
|
28
|
July 7, 2025
|
|
Restraining Solvent Molecules Under an Ice Slab
|
|
0
|
27
|
July 6, 2025
|
|
Clarification on Iodide Parameters for CHARMM36 in GROMACS
|
|
0
|
29
|
June 30, 2025
|
|
Simulation with a 3 fs timestep
|
|
0
|
31
|
June 30, 2025
|
|
Help with Pulling Simulation Between Two Atoms
|
|
1
|
20
|
June 27, 2025
|
|
NOTE 1 [file NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
|
|
5
|
1568
|
June 23, 2025
|
|
Membrane Equilibrium
|
|
3
|
30
|
June 2, 2025
|
|
PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
|
|
0
|
12
|
May 26, 2025
|