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PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
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2
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45
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July 30, 2026
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Parametrization of pyroglutamate
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2
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43
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July 28, 2026
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Simulation of a dizinc metallo protein
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6
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516
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July 24, 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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57
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July 4, 2026
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How to determine b0 and kb in Zn-coordinated bond
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0
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30
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July 2, 2026
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Protein small molecule simulation
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3
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71
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June 25, 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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46
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June 24, 2026
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What if the protein contains mutations and missing residues?
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2
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88
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June 4, 2026
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Is there a way to perform simulations with less standard addatives?
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3
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55
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June 1, 2026
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DCLE diffuse into Bulk solution from membrane after 1.8 ns equilbration in HMMM (Charmm-Gui)
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0
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33
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May 26, 2026
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Simulation box size?
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7
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120
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May 19, 2026
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COM motion removal during NVT simulation with electric field
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5
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92
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May 19, 2026
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LINCS Error in production run
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2
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142
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May 1, 2026
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PBC/trajectory reconstruction problem for discontinuous multi-chain RNA fragment
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0
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22
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April 28, 2026
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One system not plateauing in NPT before SMD comparison across multiple complexes
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0
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27
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April 28, 2026
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New atomipy online molecular builder for inorganic/geochemical based systems
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0
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40
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April 26, 2026
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GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2
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0
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37
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April 25, 2026
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Covalent bound PLP to SPT (membrane bound)
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0
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40
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April 22, 2026
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Simulating a protein or DNA with multiple ligands
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2
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70
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April 7, 2026
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Obtaining parameters for ligands in a nanoparticle assembly
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0
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43
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April 5, 2026
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Virtual site creation
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0
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29
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April 5, 2026
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Multicomponent system
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1
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63
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April 1, 2026
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Simulation of polypropylene huntite melt!
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0
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18
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April 1, 2026
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Problem using Position restraints for multiple groups
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2
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59
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March 30, 2026
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Pathogen membrane and peptides simulation
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4
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92
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March 29, 2026
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Steered Molecular dynamics of a ligand moving towards bilayer membrane
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1
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66
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March 16, 2026
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Flat-bottom restraints on specific atoms
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3
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46
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March 10, 2026
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Steered MD Simulation error
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19
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295
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February 19, 2026
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CGenFF ERROR - attype warning: unknown sulfur type (SD) not supported; skipped molecule
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2
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329
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February 16, 2026
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SMD simulation - protein pulling and resulting rotation
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2
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102
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February 10, 2026
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