Help with simulated annealing of a small peptide
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1
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70
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February 20, 2024
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Dumps in protein_lig of RMSD after MD Simulations
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11
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83
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February 17, 2024
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Implausible values in free energy calculations
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4
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167
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February 16, 2024
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Simulating a Protein-Ligand dimer
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6
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212
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February 16, 2024
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Simulation breaks the side chain of some residue gromacs
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4
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160
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February 15, 2024
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Removal of one leaflet causing errors in trajectory
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3
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40
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February 14, 2024
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Wall simulations with GPU
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6
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215
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February 13, 2024
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Mdrun aborts without notification and doesnt produce the expected output
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2
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77
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February 12, 2024
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Flat bottomed position restraints as center of mass position restrains
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1
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82
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February 8, 2024
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Mdrun issue - well known issue but still cant fix it
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4
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96
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February 7, 2024
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No run after gmx mdrun
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10
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185
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February 6, 2024
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Fatal error: number of coordinates in coordinate file does not match topology file
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2
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189
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February 3, 2024
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Domain Decomposition Error
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2
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232
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February 3, 2024
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Issue of High Potential Energy on Running Minimization
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9
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188
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February 1, 2024
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Error in user input: Required option was not provided, and the default file 'topol' does not exist
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3
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80
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February 1, 2024
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hipSYCL Error when running with multiple MPIs
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11
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260
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January 30, 2024
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Why Fatal error: Unexpected cudaStreamQuery failure happend in gromacs2019?
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27
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570
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January 30, 2024
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Unevern spikes in RMSD graphs after MD simulations
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5
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451
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January 29, 2024
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Automatic reduction of energy terms with DD
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1
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64
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January 29, 2024
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LINCS warning system crash--changing MPI and OpenMP threads helps going further
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4
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481
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January 27, 2024
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Poor performance of simulation with Colvars module in GROMACS 2024.1 beta
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12
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171
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January 26, 2024
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Gromacs: mpirun noticed that process rank 63 with PID 0 on node *** exited on signal 11
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2
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209
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January 26, 2024
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The system of protein-DNA was unstable and said "Segmentation fault" when i run NPT MD using gromacs
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4
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115
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January 25, 2024
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My topology file uses atom names for ions, not molecules. I can't see errors?
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1
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84
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January 25, 2024
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LINCS warning during energy minimizations
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8
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1156
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January 24, 2024
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Continuing simulation after timeout
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1
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79
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January 24, 2024
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Offloading NB and PME to GPUs in multi-sim run
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1
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81
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January 22, 2024
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Mdrun 2024Seqmentation fault%
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1
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87
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January 22, 2024
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Breaking a ligand with umbrella sampling
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5
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91
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January 21, 2024
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Gromacs not utilizing gpu
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6
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328
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January 20, 2024
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