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Obtaining parameters for ligands in a nanoparticle assembly
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0
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24
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April 5, 2026
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Simulation of polypropylene huntite melt!
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0
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5
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April 1, 2026
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PEG2000 collapsing into bilayer core in atomistic simulation (GROMOS 53A6)
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0
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19
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March 19, 2026
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Amber FF parameters for metal binding centres
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4
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1309
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March 17, 2026
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Newest CHARMM36 port for GROMACS
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39
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24137
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March 5, 2026
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Amber19SB and Amber14SB in old versions of Gromacs
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13
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230
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February 27, 2026
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Define ATP+mg in Amber forcefield
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0
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30
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February 23, 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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Amber99sb-ildn ff with Hydroxyproline
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1
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44
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February 10, 2026
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How to build Ligand topology
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2
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90
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February 4, 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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How to add hydrogen atoms to the complex with correct coordinates?
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2
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26
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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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48
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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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60
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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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38
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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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44
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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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60
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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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14
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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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557
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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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109
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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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155
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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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91
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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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Query regarding making all .mdp files for ionization, equllibration, energy minimization
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2
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45
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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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115
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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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59
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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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531
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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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48
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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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62
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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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18
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October 12, 2025
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