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Adding Bond Connection 2'-5' RNA
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0
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17
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October 21, 2026
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Chloroform as a solvent in Charmm36 force field
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4
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316
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October 18, 2026
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How create uneven box for all-atom simulation
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4
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48
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October 15, 2026
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Position restraints and mdp setup after an AmberTools(ZAFF) -> ParmEd -> GROMACS handover
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0
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37
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October 13, 2026
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Mdp file differences between CHARMM27 and CHARMM36 parameters
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4
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95
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October 7, 2026
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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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93
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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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62
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August 10, 2026
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Parametrization of pyroglutamate
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2
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73
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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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608
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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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90
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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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43
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July 2, 2026
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Protein small molecule simulation
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3
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88
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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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69
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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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137
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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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71
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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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41
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May 26, 2026
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Simulation box size?
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7
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185
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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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149
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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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172
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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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38
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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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38
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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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84
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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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51
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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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56
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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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97
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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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53
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April 5, 2026
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Virtual site creation
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0
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33
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April 5, 2026
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Multicomponent system
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1
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77
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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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27
|
April 1, 2026
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Problem using Position restraints for multiple groups
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2
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82
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March 30, 2026
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