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Steered MD Simulation error
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11
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73
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February 11, 2026
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SMD simulation - protein pulling and resulting rotation
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2
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21
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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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46
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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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38
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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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25
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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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20
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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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44
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January 21, 2026
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Water box elongation
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1
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24
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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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43
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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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27
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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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62
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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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318
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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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52
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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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76
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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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56
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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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24
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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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47
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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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38
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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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33
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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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59
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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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42
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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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64
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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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121
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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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153
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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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43
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November 10, 2025
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GROMACS number of molecules
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0
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18
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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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61
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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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327
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October 26, 2025
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ZINK in Protein
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4
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93
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October 21, 2025
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