|
Problems with generating self contained topology file (necessary for partial tempering with plumed)
|
|
1
|
6
|
September 29, 2025
|
|
RMSD graph after protein protein md simulation
|
|
4
|
61
|
September 8, 2025
|
|
Molecule type 'Protein_chain_A' contains no atoms
|
|
1
|
43
|
June 2, 2025
|
|
Need help minimising a backmapped system (I used backward method)
|
|
0
|
16
|
May 12, 2025
|
|
Number of coordinates did not match in coordinated file with the topology file
|
|
24
|
9775
|
May 1, 2025
|
|
No default bond types, rykaert bell types and more
|
|
1
|
24
|
March 24, 2025
|
|
No default Position Rest. graphene sheet
|
|
0
|
26
|
March 16, 2025
|
|
[MD Simulation Error] Fatal PME Rank Issue: Particles Moving Out of Domain Decomposition Cell
|
|
2
|
54
|
March 4, 2025
|
|
The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance
|
|
17
|
6993
|
February 5, 2025
|
|
"No default Bond types" error during grompp for specbond.dat bonds
|
|
0
|
24
|
January 29, 2025
|
|
No default U-B Types
|
|
0
|
91
|
January 16, 2025
|
|
Warning: atom name in .top and .gro does not match
|
|
2
|
153
|
January 23, 2025
|
|
Invalid order for directive atomtypes (error)
|
|
17
|
9119
|
January 13, 2025
|
|
No default improper dihedral types in Amber ff14sb-OL21 for DNA simulations
|
|
2
|
127
|
December 22, 2024
|
|
Error: Topol.top file doesn`t match solv.gro file
|
|
1
|
68
|
December 18, 2024
|
|
Issues with MD Run and Fe Displacement in Hemoglobin Simulation
|
|
4
|
101
|
December 13, 2024
|
|
ERROR 164 [file topol.top, line 100195]: No default Ryckaert-Bell. types
|
|
3
|
68
|
November 29, 2024
|
|
Energy minimization error sc-r-power = 48 not supported
|
|
4
|
702
|
November 18, 2024
|
|
Ligand MD simulation
|
|
2
|
58
|
November 8, 2024
|
|
Grompp errors with v2024.3: The drift estimate should be a finite value
|
|
5
|
40
|
October 30, 2024
|
|
Fatal error: Syntax error - File ffnonbonded.itp, line 5 Last line read: '[ atomtypes ]' Invalid ord
|
|
5
|
107
|
October 29, 2024
|
|
Reading double precision coordinate data with grompp
|
|
7
|
39
|
October 25, 2024
|
|
Velocity distribution and
|
|
0
|
25
|
October 15, 2024
|
|
Error in using the soft core minimization
|
|
4
|
231
|
September 24, 2024
|
|
Largest distance between excluded atoms error even though atoms are bonded
|
|
0
|
177
|
September 11, 2024
|
|
Check the Forcefield of the electrolyte system EC DEC DMC
|
|
1
|
50
|
September 9, 2024
|
|
Error in NPT Equilibration for Protein Ligand Complex MD Tutorial
|
|
3
|
339
|
August 28, 2024
|
|
For two ligand and a complex molecular dynamics simulation in GROMACS
|
|
2
|
96
|
August 15, 2024
|
|
Dihedral bonds disappearing/ignored during GROMPP step
|
|
10
|
51
|
August 14, 2024
|
|
Another Problem with Distances Between Pull Groups
|
|
3
|
726
|
July 14, 2024
|