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Simulating a protein or DNA with multiple ligands
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2
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31
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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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25
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April 5, 2026
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Virtual site creation
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0
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18
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April 5, 2026
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Multicomponent system
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1
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37
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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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7
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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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30
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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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58
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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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29
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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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20
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March 10, 2026
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Steered MD Simulation error
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19
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148
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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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289
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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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49
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February 10, 2026
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Your Review on AMBER19sb MD in GROMACS2026
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1
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112
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February 4, 2026
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The contradiction between the mdp settings and the real pull rate
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13
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64
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February 4, 2026
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Simulated annealing of protein-DNA complex
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0
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45
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February 3, 2026
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How to add hydrogen atoms to the complex with correct coordinates?
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2
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28
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January 23, 2026
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Pdb2gmx rounds up the charge of a single atom
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7
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49
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January 21, 2026
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Charge precision in topology files: parsing behaviour and validation tolerance
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5
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62
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January 21, 2026
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Water box elongation
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1
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26
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January 21, 2026
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Steered MD Simulation using Gromacs
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2
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66
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January 7, 2026
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High pressure in x and y axis in a buble in a nano channel
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2
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34
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January 5, 2026
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Should I manually set -ntomp 16 or let Gromacs auto-configure its settings？
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4
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105
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December 29, 2025
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Best practice for using newer AMBER force fields (ff19SB) in GROMACS?
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3
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563
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December 17, 2025
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Steered molecular dynamics - umbrella samling
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1
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75
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December 8, 2025
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How to add terminal caps in AMBER with GROMACS
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1
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156
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December 3, 2025
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INSANE not compatible with martini3 GM3?
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1
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95
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December 1, 2025
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Simulating a Reverse Transcriptase complex with RNA, DNA
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1
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43
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December 1, 2025
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Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file 'complex.top'
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2
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61
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November 29, 2025
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Dimeric protein handling during simulation
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1
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68
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November 27, 2025
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RNA simulation error with phosphate group atoms of the first nucleotide
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3
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60
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November 26, 2025
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