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Steered molecular dynamics - umbrella samling
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1
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25
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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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23
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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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29
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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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11
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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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19
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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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23
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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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23
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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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35
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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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24
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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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45
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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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80
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November 20, 2025
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Best practice for using newer AMBER force fields (ff19SB) in GROMACS?
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2
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105
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November 19, 2025
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Simulate the freezing of saline under an external electric field
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12
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78
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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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29
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November 10, 2025
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GROMACS number of molecules
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0
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15
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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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53
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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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160
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October 26, 2025
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ZINK in Protein
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4
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61
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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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39
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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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26
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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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28
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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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28
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October 14, 2025
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GROMACS 2025.3 CUDA 13 RTX 5070 Ti Fails on Simulations
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2
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57
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October 14, 2025
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Performance of SMD simulation
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1
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36
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October 10, 2025
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How to simulate a cyclic protein with AMBER99SB ff?
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1
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30
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October 9, 2025
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Tools for creating initial .gro and combining source files
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0
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18
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October 8, 2025
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what should do with zink-protein.pdf to get topology file?
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5
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46
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October 7, 2025
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Help: RTX 5080 (Blackwell, Compute Capability 12.1) + WSL2 + CUDA 13.0 “No Kernel Image Available”
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2
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172
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October 5, 2025
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Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
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2
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44
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October 5, 2025
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How should I choose the box size for nanodisc simulations?
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1
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29
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October 3, 2025
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