Free energy of specific bond breaking/formation through thermodynamic integration
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4
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20
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November 12, 2024
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MD Simulation for Small Molecule aggregation
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1
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13
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November 12, 2024
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Solvate creates mismatch in atom numbering with topology file
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1
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7
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November 12, 2024
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Help, adding PEG to my gro and top file-is not placed where it should be
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3
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15
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November 12, 2024
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Unbalanced CPU and GPU Utilization in GROMACS
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1
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17
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November 9, 2024
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Error in pdb2gmx with non standard residue
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3
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87
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November 8, 2024
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Ligand MD simulation
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2
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19
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November 8, 2024
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[Solved] How long should I wait to have two time decorrelated LJ simulations of 8000 atoms?
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4
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25
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November 6, 2024
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Hbond issue with molecule
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1
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21
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October 30, 2024
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LINCS Error in production run
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1
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13
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October 29, 2024
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I want to generate the system between short protein and membrane LIPID21 forcefield
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1
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13
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October 28, 2024
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Is there a way to use specbond.dat without changing the original file in the gromacs directory?
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1
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10
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October 28, 2024
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No default Improper Dih. types
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3
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29
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October 24, 2024
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How to determine the amount of solvent added to the simulation box?
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3
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927
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October 21, 2024
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Error in the coordinate file sol.gro and topol.gro
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1
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30
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October 19, 2024
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GROMACS benchmark on 33 GPUs
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0
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24
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October 17, 2024
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How to construct suitable recombinant protein structure for molecular dynamics simulation?
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0
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11
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October 14, 2024
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BOX SIZE CHANGE
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4
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41
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October 13, 2024
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Troubleshooting a GROMACS termination following "Generating 1-4 interactions: fudge = 1"
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0
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23
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October 11, 2024
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Error: No Default LJ-14 Types When Integrating Small Molecule into GAFF+GLYCAM System
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4
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37
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October 10, 2024
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Force field for Magnesium
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1
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27
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October 8, 2024
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Do we need position restraints for deformation simulations?
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0
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24
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October 7, 2024
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Running an NPT simulation after NVT (domain decomposition error)
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3
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53
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October 7, 2024
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Charmm-feb2021_caps.ff
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0
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8
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October 6, 2024
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I tried to perform energy minimization using "http://www.mdtutorials.com/gmx/lysozyme/05_EM.html"
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1
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8
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October 5, 2024
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Breaking of the molecular structure after energy minimization
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3
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23
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October 4, 2024
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Gas Phase Minimization
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1
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21
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October 1, 2024
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Complex protein ligand Issue
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1
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25
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October 1, 2024
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SD integrator vs MD integrator
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6
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79
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September 30, 2024
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Position restraints for Umbrella sampling simulation of membrane protein-ligand
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5
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74
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September 30, 2024
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