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Speed up "rdf" and "hbond-legacy" for single frames for whole trajectory?
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0
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17
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January 16, 2025
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How to put distance restraints into topology file
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25
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1037
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January 16, 2025
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How can I add molecules to an equilibrated system without messing PBCs?
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1
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19
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January 16, 2025
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Chloroform as a solvent in Charmm36 force field
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1
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85
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January 16, 2025
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How to calculate interface coverage by a polymer?
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0
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14
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January 16, 2025
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Performing MD for a protein-ligand complex where the protein is tetramer
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0
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30
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January 16, 2025
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Estimated Oscillation Time period less than timestep
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4
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54
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January 15, 2025
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.m2p file format
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1
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18
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January 15, 2025
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Imposing restraints between protein and ligand
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22
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1466
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January 15, 2025
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Excluded distance larger than cutoff in ligand with virtual site
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17
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193
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January 15, 2025
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Could NOT find CUDA (missing: CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
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0
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88
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January 15, 2025
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Issue with correcting PBC for DNA Separation in GROMACS
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7
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48
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January 15, 2025
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How to analyze .nc or .dcd trajectory files in GROMACS
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2
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70
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January 15, 2025
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Is it possible to make angle restraints between two values?
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3
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735
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January 15, 2025
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Retaining or removing ions and crystallographic waters in PDB files
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4
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62
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January 15, 2025
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Curve in water MSD
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8
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67
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January 14, 2025
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MD of multiple ligands with charmm36 force field
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1
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340
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January 14, 2025
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how to analyze .nc or .dcd trajectory files in GROMACS
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1
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17
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January 14, 2025
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Free Energy Calculation general questions and LINCS Warning
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10
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1417
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January 13, 2025
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Hardware advice for maximizing throughput (CpHMD/Replica Exchange)
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0
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20
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January 13, 2025
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Does anyone have validated GAFF parameters for the PEG400?
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0
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10
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January 13, 2025
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Invalid order for directive atomtypes (error)
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17
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8661
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January 13, 2025
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Why deformation simulation produce Young's modulus significantly different from experimental value?
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10
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141
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January 13, 2025
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Required for NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site)
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2
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15
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January 13, 2025
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Simulated Annealing of Ethanol water biphasic system
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3
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31
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January 13, 2025
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Gromacs simulation for water splitting
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0
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8
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January 12, 2025
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Modified amino acid in charmm forcefield
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4
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1046
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January 11, 2025
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Problem with Introduction to Molecular Dynamics tutorial
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4
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51
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January 11, 2025
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RMSD shoots up
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17
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1505
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January 11, 2025
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Failed to visualise the bonds between two beads of coarse-grained model in vmd software
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2
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37
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January 11, 2025
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