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PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
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3
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78
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September 2, 2026
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Topology and force-field parameters for Rhodamine B in water
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0
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50
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August 10, 2026
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Parametrization of pyroglutamate
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2
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62
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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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575
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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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80
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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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36
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July 2, 2026
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Protein small molecule simulation
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3
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78
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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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59
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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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118
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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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64
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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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37
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May 26, 2026
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Simulation box size?
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7
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154
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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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129
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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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162
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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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28
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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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31
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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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47
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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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44
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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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46
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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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84
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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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46
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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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69
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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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19
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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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70
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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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107
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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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75
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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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71
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March 10, 2026
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Steered MD Simulation error
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19
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315
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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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345
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February 16, 2026
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