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How to generate a MOL2 ligand file with the correct docking pose, full hydrogens, and physiological
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1
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58
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July 1, 2026
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Efficient Workflow for Multiple Modified Residues
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2
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47
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July 1, 2026
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Ligand jumping around during GROMACS MD simulation after CHARMM-GUI setup – PBC issue or system prep
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1
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26
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June 26, 2026
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Gromacs 2025.4 + Plumed 2.10 Installation issue
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0
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36
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June 26, 2026
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Trying to perturb a torsion with multiple terms
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1
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28
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June 25, 2026
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Protein small molecule simulation
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3
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74
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June 25, 2026
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Temperature coupling
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3
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82
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June 24, 2026
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Standard publishable preprocessing of AlphaFold3 complex structures for GROMACS MD simulations
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0
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51
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June 24, 2026
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Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding
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1
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38
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June 24, 2026
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Fatal Error: no domain decomposition for rank 4, min cell size 1.776 nm
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1
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33
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June 24, 2026
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GROMACS pdb2gmx Warning: Missing Atoms (H and O) in AlphaFold3-Derived TCR–pMHC Structure
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1
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33
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June 24, 2026
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TIP4P/2005 water model
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2
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596
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June 22, 2026
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Run gmx energy on a large number of systems
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2
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42
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June 18, 2026
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Questions about inter domain/chain distance restraint
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0
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23
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June 17, 2026
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[Help] Seeking MDP files for graphene oxide / phenol / water adsorption system
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0
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28
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June 16, 2026
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WT vs mutant protein-protein complex MD: should mutant be generated from WT docked complex or redock
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0
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27
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June 15, 2026
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Forcefield for guanidium acetate
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0
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31
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June 12, 2026
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Surface tension calculation of gas-liquid interface
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2
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209
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June 12, 2026
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Polymer expansion instead of compression when using wall potential in Gromacs?
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6
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69
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June 12, 2026
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IFT in CG simulation using MARTINI 3.0
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1
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48
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June 12, 2026
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Charmm36 and lj-pme setting
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2
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92
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June 12, 2026
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Shear Viscosity Calculation for Isotropic Molecules
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7
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102
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June 9, 2026
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Deform by Gromacs to apply shear rate
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8
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2612
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June 9, 2026
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ForceField for Intrisically disordered protein
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14
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159
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June 8, 2026
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Statistical Analysis Method for Peak force and total work in Steered molecular dynamics
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3
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68
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June 4, 2026
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What if the protein contains mutations and missing residues?
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2
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101
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June 4, 2026
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Gmx anaeig problematic error "Dimensions in the eigenvector files don't match"
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4
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68
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June 3, 2026
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Modified dihedral notation
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6
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80
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June 3, 2026
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Convert amber to gromacs
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0
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58
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June 2, 2026
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Force Field-angle
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2
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47
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June 1, 2026
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