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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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Pdb2gmx not recognizing water block
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1
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31
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November 11, 2025
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Assertion failed for buckingham interacting solid
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1
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14
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October 28, 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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165
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October 26, 2025
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How to simulate a cyclic protein with AMBER99SB ff?
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1
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32
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October 9, 2025
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Problems with generating self contained topology file (necessary for partial tempering with plumed)
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1
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26
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September 29, 2025
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RMSD graph after protein protein md simulation
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4
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86
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September 8, 2025
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Molecule type 'Protein_chain_A' contains no atoms
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1
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54
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June 2, 2025
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Need help minimising a backmapped system (I used backward method)
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0
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18
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May 12, 2025
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Number of coordinates did not match in coordinated file with the topology file
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24
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9929
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May 1, 2025
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No default bond types, rykaert bell types and more
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1
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29
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March 24, 2025
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No default Position Rest. graphene sheet
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0
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30
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March 16, 2025
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[MD Simulation Error] Fatal PME Rank Issue: Particles Moving Out of Domain Decomposition Cell
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2
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72
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March 4, 2025
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The largest distance between excluded atoms is 1.725 nm, which is larger than the cut-off distance
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17
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7207
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February 5, 2025
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"No default Bond types" error during grompp for specbond.dat bonds
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0
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32
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January 29, 2025
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No default U-B Types
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0
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120
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January 16, 2025
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Warning: atom name in .top and .gro does not match
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2
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208
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January 23, 2025
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Invalid order for directive atomtypes (error)
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17
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9431
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January 13, 2025
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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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181
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December 22, 2024
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Error: Topol.top file doesn`t match solv.gro file
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1
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84
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December 18, 2024
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Issues with MD Run and Fe Displacement in Hemoglobin Simulation
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4
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123
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December 13, 2024
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ERROR 164 [file topol.top, line 100195]: No default Ryckaert-Bell. types
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3
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100
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November 29, 2024
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Energy minimization error sc-r-power = 48 not supported
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4
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718
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November 18, 2024
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Ligand MD simulation
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2
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68
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November 8, 2024
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Grompp errors with v2024.3: The drift estimate should be a finite value
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5
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53
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October 30, 2024
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Fatal error: Syntax error - File ffnonbonded.itp, line 5 Last line read: '[ atomtypes ]' Invalid ord
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5
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140
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October 29, 2024
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Reading double precision coordinate data with grompp
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7
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51
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October 25, 2024
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Velocity distribution and
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0
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31
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October 15, 2024
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Error in using the soft core minimization
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4
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265
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September 24, 2024
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Largest distance between excluded atoms error even though atoms are bonded
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0
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195
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September 11, 2024
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