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How to add hydrogen atoms to the complex with correct coordinates?
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2
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88
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January 23, 2026
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Tabulated nonbonded potentials in GROMACS 2026
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1
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117
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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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111
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January 21, 2026
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Gromacs .hdb format RU5 case study
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3
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73
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January 14, 2026
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Conducting MD simulation on a zinc metalloprotein with 4 zinc ions
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0
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118
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January 7, 2026
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Is it possible to add other form of lennard jones potential form (such as LJ9-3, LJ6-3) in gromacs?
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3
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119
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January 7, 2026
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Does GROMACS distinguish Rp/Sp chiral phosphate modifications at O1P vs O2P in DNA?
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0
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23
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January 5, 2026
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Best practice for using newer AMBER force fields (ff19SB) in GROMACS?
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3
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1073
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December 17, 2025
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Adding external gpu force to gromacs result in energy conservation problem
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8
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198
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December 10, 2025
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How to add terminal caps in AMBER with GROMACS
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1
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262
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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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160
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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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73
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December 1, 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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70
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November 25, 2025
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Calculation of Coulomb 1-4 energies and Coulomb SR energies
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5
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188
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November 24, 2025
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Adding missing dihedral interactions to a Force Field
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1
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100
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October 31, 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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965
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October 26, 2025
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A Custom Water Force Field Implementation
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0
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58
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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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101
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October 14, 2025
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Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?
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0
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32
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October 12, 2025
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How to simulate a cyclic protein with AMBER99SB ff?
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1
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96
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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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39
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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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162
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October 7, 2025
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Requesting for claud computing system for md production
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2
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51
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October 7, 2025
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mRNA forcefields issue
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0
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51
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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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119
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October 5, 2025
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Inaccurate thermostatting when simulating MD water
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1
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149
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October 4, 2025
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x2top for MINFF
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0
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97
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October 2, 2025
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How to set up protein–peptide complex simulation in GROMACS: peptide as ligand or whole complex?
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1
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214
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September 29, 2025
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Amber04 forcefield check in gromacs
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1
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131
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September 23, 2025
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gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS
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0
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199
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September 21, 2025
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