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Zero OPLS Lennard-Jones parameters for H atoms and overlapping atoms
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5
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774
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January 24, 2025
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Protonation States in the OPLS-AA Forcefield
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0
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5
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January 24, 2025
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How to perform md simulation on a protein structure which have a ca+ ions
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0
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8
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January 23, 2025
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Topology of an ACE-linked cyclic peptide with a free C-ter
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0
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6
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January 23, 2025
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Parametrization of DNA Backbone with Alkyl Chain Using CHARM and Non-Integer Charge Issue
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0
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5
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January 22, 2025
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DNA Backbone Parametrization and rtp File
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1
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25
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January 20, 2025
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NPT Step Issue with Protein 1QS4 (4 Waters and Mg²⁺ in Active Site)
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4
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24
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January 22, 2025
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How to use the charmm36 force field parameters from CGenFF for ligand?
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1
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40
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January 21, 2025
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Issue with pdb2gmx when peptide is capped
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4
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18
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January 21, 2025
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Questions About CHARMM36 Parameters for DNA Systems
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2
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24
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January 17, 2025
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Help, adding PEG to my gro and top file-is not placed where it should be
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4
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30
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January 17, 2025
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Chloroform as a solvent in Charmm36 force field
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1
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29
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January 16, 2025
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Estimated Oscillation Time period less than timestep
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4
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23
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January 15, 2025
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Does anyone have validated GAFF parameters for the PEG400?
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0
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4
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January 13, 2025
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Adding an organic molecule to OPLS-AA force field
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0
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20
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January 11, 2025
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Ion Parameters in Amber99bsc1 Force Field
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0
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7
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January 10, 2025
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On FF parameterization of molecules with non-zero valence
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3
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11
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January 10, 2025
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How to use Clay.ff with gromacs for molecular dynamics simulation of mica
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2
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24
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January 8, 2025
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Using the Martini3 Forcefield in pdb2gmx
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2
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31
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January 7, 2025
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Pressure off due missing LJ parameters
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4
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25
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January 7, 2025
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Charmm36 ff with PTM on GROMACS
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3
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16
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January 5, 2025
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Inserting a modified residue into a protein/DNA chain using pdb2gmx
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34
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1459
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December 27, 2024
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Membrane Protein ligand simulation
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6
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44
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December 27, 2024
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No default improper dihedral types in Amber ff14sb-OL21 for DNA simulations
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2
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37
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December 22, 2024
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Error in residue topology database
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1
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20
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December 19, 2024
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Error: Topol.top file doesn`t match solv.gro file
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1
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23
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December 18, 2024
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Easily lookup the origin of the opls_XXX atom types?
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1
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20
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December 18, 2024
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gmx_MMPBSA order of the molecules in the pdb file and topology file
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0
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15
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December 17, 2024
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Issues with MD Run and Fe Displacement in Hemoglobin Simulation
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4
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50
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December 13, 2024
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How to implement Stillinger-Weber (SW) Three-Body Interaction in GROMACS?
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1
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18
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December 11, 2024
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