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Steered MD Simulation error
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5
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29
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January 29, 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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19
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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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40
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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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42
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January 21, 2026
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Water box elongation
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1
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20
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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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37
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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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24
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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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60
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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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260
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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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45
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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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61
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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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45
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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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20
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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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39
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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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35
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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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28
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November 26, 2025
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Box explodes using NPT.mdp
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2
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53
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November 26, 2025
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Query regarding making all .mdp files for ionization, equllibration, energy minimization
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2
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36
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November 25, 2025
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Query:Reagrding using the multiple nodes's GPU or CPU to run MD production step in gromacs
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4
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61
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November 20, 2025
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How to determine the number of water molecules in a box? gmx insert-molecules or gmx solvate?
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8
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106
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November 20, 2025
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Simulate the freezing of saline under an external electric field
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12
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143
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November 13, 2025
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Non-Bonded parameters definition not working
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2
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40
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November 10, 2025
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GROMACS number of molecules
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0
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16
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November 8, 2025
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Free-energy on virtual sites only (or vice versa)
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2
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59
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October 29, 2025
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How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
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9
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259
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October 26, 2025
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ZINK in Protein
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4
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87
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October 21, 2025
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Umbrella sampling PMFs with additional restraints
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0
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51
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October 20, 2025
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Water accumulation in slab geometry
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0
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35
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October 20, 2025
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A Custom Water Force Field Implementation
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0
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34
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October 17, 2025
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Modify residues using CHARMM-GUI pdb reader and manipulator
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0
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39
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October 14, 2025
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