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Problem with gromacs script generetated with charmm-gui
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2
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7
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July 29, 2025
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Pull code on a long filament
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0
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3
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July 29, 2025
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Insert the simulation box
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0
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3
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July 29, 2025
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Problem with adding ions
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1
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6
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July 28, 2025
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High LJ (SR) in graphene sheet minimization
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0
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6
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July 28, 2025
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Issues when equilibrating a membrane system with 2024.4 (not present in 2023.3)
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1
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25
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July 22, 2025
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Gen_vel=no and continuation=false
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3
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164
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July 22, 2025
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.pdb and .top file
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0
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12
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July 22, 2025
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Homocysteine covalently bonded with a protein MD simulation how to perform
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0
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12
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July 21, 2025
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Computational Electrophysiology Setup with GROMACS (.mdp file)
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3
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231
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July 19, 2025
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Free Energy Calculation of Tryptophan
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1
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23
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July 18, 2025
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Equilibration of new lipid model
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0
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9
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July 16, 2025
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How to create restrained file for sol
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0
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10
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July 15, 2025
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Flat-bottom position restraints on water molecules
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5
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27
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July 7, 2025
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How to simulate the specific residues by mentioning their position in the sequence?
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0
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16
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July 3, 2025
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How to prepare nucleotides for MD simulation?
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0
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23
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June 26, 2025
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Backmapping from coarse grain to all atom
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3
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58
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June 26, 2025
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Forcefield to simulate RNA molecules containing modifications with GROMACS and amber ff
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2
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387
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June 20, 2025
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Is it possible to use an eam potential?
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2
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23
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June 5, 2025
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Umbrella-sampling setup of molecule permeation through interface surfactant membrane
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20
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238
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June 4, 2025
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Membrane Equilibrium
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3
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24
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June 2, 2025
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PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
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0
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10
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May 26, 2025
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Mdrun crashes with some md parameter during NPT (gmx compiled for rocm,AdaptiveCPP)
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8
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76
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May 22, 2025
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Studying Zn2+ tetrahedal coordination stability
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0
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19
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May 21, 2025
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How to correctly define disulfide bonds in GROMACS?
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0
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37
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May 20, 2025
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System has non-zero total charge: -1.000000
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1
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26
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May 19, 2025
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Potentials on gromacs
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0
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13
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May 16, 2025
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Splitting 100ns Gromacs runs into 25ns smaller chunks
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0
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32
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May 19, 2025
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SMD Pulling of DNA Toward Asymmetric Bilayer
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18
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177
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May 17, 2025
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How to solve "No default bond types for interaction"
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0
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7
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May 16, 2025
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