|
Is it possible to extract coordinates from a .cpt file?
|
|
3
|
11
|
December 5, 2025
|
|
Possible HIS inconsistency in Gromacs CpHMD example
|
|
0
|
24
|
October 24, 2025
|
|
Should I swap group order and sum results for hydrogen bond counts when using `gmx hbond`?
|
|
0
|
22
|
October 5, 2025
|
|
Energy minimizing multiple frames of an MD trajectory
|
|
0
|
20
|
September 12, 2025
|
|
Charge Rounding-Off Error
|
|
0
|
19
|
July 1, 2025
|
|
Compilation of the latest GROMACS (2025.2) with cuDSS support
|
|
0
|
18
|
June 25, 2025
|
|
Topology NON-BONDING parametersproblems
|
|
0
|
18
|
May 16, 2025
|
|
Need help minimising a backmapped system (I used backward method)
|
|
0
|
18
|
May 12, 2025
|
|
How to Calculate Coordination Numbers at the Interface and in the Bulk Separately?
|
|
0
|
19
|
April 12, 2025
|
|
Assistance with Fixing a Spherical Structure in Umbrella Sampling
|
|
0
|
22
|
March 17, 2025
|
|
Peptide Simulation
|
|
0
|
19
|
February 27, 2025
|
|
RMSD graphs
|
|
0
|
18
|
February 13, 2025
|
|
1-4 interactions not tallying
|
|
0
|
20
|
December 20, 2024
|
|
Recommended way to thermostat a system where one covalently-bound component is fully restrained
|
|
2
|
15
|
December 5, 2025
|
|
Clarification on gmx select moltype syntax in GROMACS 2025.3
|
|
0
|
21
|
October 30, 2025
|
|
Radial distribution function calculation parameter rmax selection
|
|
0
|
18
|
October 15, 2025
|
|
Tools for creating initial .gro and combining source files
|
|
0
|
18
|
October 8, 2025
|
|
How to determine the number of Hydrogen bonds between the amide H and carbonyl oxygen
|
|
0
|
17
|
September 28, 2025
|
|
Why Does GROMACS Rename a DG Terminus to DG5 Without Manual Patching?
|
|
0
|
19
|
July 22, 2025
|
|
Number of digits in rdf data
|
|
0
|
18
|
July 14, 2025
|
|
How to simulate the specific residues by mentioning their position in the sequence?
|
|
0
|
18
|
July 3, 2025
|
|
Constrain receptor ligand
|
|
0
|
18
|
June 28, 2025
|
|
How to prepare nucleotides for MD simulation?
|
|
0
|
26
|
June 26, 2025
|
|
MD simulations of protein on muscovite mica
|
|
0
|
23
|
May 13, 2025
|
|
Failed to run long trajectory to compute MSD
|
|
0
|
17
|
February 27, 2025
|
|
Constant Surface Tension Simulation
|
|
0
|
22
|
February 26, 2025
|
|
Gmx chi Alanine residues output
|
|
1
|
15
|
November 30, 2025
|
|
The amino acids reported as errors by pdb2gmx do not correspond to the amino acids in the structure
|
|
1
|
13
|
September 19, 2025
|
|
Assistance with “Scattered Bound Ion Issue” in GROMACS Trajectory Extraction
|
|
1
|
19
|
January 27, 2025
|
|
High potential energy
|
|
0
|
16
|
October 26, 2025
|
|
Workflow for incorporating a modified residue into a protein through CHARMM-GUI
|
|
0
|
17
|
June 12, 2025
|
|
Error While running npt equillibration of last frames extracted form complex
|
|
0
|
19
|
May 22, 2025
|
|
GROMACS Tutorial Protein-Ligand Complex question
|
|
0
|
19
|
February 18, 2025
|
|
Pairs and triplets in ndx file for gmx gangle
|
|
0
|
20
|
February 11, 2025
|
|
Missing Dihedral Types and Ion Addition Issue in GROMACS
|
|
0
|
16
|
January 18, 2025
|
|
Zinc problem while running pdb2gmx
|
|
0
|
18
|
November 8, 2025
|
|
Part of the protein structure breaks after Energy Minimization
|
|
0
|
21
|
November 6, 2025
|
|
Resuming run with -cpi fails when launched with mpiexec.hydra -np $SLURM_NPROCS
|
|
0
|
17
|
October 16, 2025
|
|
Density is reducing after nvt equilibration follwed by md production
|
|
0
|
17
|
August 19, 2025
|
|
High LJ (SR) in graphene sheet minimization
|
|
0
|
16
|
July 28, 2025
|
|
SMD simulation using gold nano particle
|
|
0
|
29
|
July 26, 2025
|
|
Number of water cluster in gromacs 2022?
|
|
0
|
18
|
June 25, 2025
|
|
Fatal error: Residue type 'NMA' not found in residue topology database
|
|
0
|
15
|
May 23, 2025
|
|
How to make dihedral force constant in CB9H10 cage boron cluster
|
|
0
|
17
|
May 21, 2025
|
|
Window spacing in drug pull
|
|
0
|
19
|
April 26, 2025
|
|
Charmm36 with GROMACS
|
|
0
|
17
|
March 31, 2025
|
|
Change in position of Histidine residue lead to difference in columb interaction energy
|
|
0
|
16
|
March 3, 2025
|
|
Charmm membrane automizing
|
|
0
|
16
|
February 20, 2025
|
|
Using dynamic indices for outputting cluster centroids
|
|
0
|
16
|
January 10, 2025
|
|
Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?
|
|
0
|
14
|
October 12, 2025
|