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Workstation options
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2
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114
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July 7, 2026
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Can CGenFF-generated partial charges differ significantly from QM-derived CHELPG (ESP) charges?
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2
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84
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July 5, 2026
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RMSD analysis of the Protein-Ligand simulation
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0
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46
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July 5, 2026
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How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction
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1
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71
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July 4, 2026
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How to deal with Zn ion in Zinc finger protein
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3
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81
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July 3, 2026
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GROMACS 2026.2 duplicate type-9 dihedral errors with CHARMM36-feb2026 and CGenFF 5.0
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1
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39
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July 3, 2026
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How to determine b0 and kb in Zn-coordinated bond
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0
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34
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July 2, 2026
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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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61
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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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48
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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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35
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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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39
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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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75
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June 25, 2026
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Temperature coupling
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3
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87
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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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55
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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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39
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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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34
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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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35
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June 24, 2026
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TIP4P/2005 water model
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2
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597
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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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28
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June 15, 2026
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Forcefield for guanidium acetate
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0
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32
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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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211
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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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72
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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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93
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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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105
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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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2621
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June 9, 2026
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