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Using H2O2 as a solvent for MD simulation
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3
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16
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September 19, 2025
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Energy drift in NVE (multiple time step algorithm)
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2
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14
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September 19, 2025
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Indexing particular residues in GROMACS
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0
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5
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September 19, 2025
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Pressure scaling more than 1%. This may mean your system is not yet equilibrated
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5
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40
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September 15, 2025
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GROMACS 2019.6 job running very slow (5 ns/day) with GPU SLURM script. How to improve performance?
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0
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10
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September 15, 2025
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RMSD graph after protein protein md simulation
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4
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54
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September 8, 2025
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SARS-CoV-2 RNA simulation
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0
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17
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September 8, 2025
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Simulation with large number of particles
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4
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18
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September 4, 2025
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How to fix negative pressure?
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9
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1339
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August 28, 2025
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How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
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0
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15
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August 28, 2025
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Pull code on a long filament
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7
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57
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August 12, 2025
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Mdrun log file error Large VCM(group MEMB)
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1
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21
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August 11, 2025
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Computing codes of GROMACS for free
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4
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74
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August 3, 2025
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Minimization of a membrane-peptide complex
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0
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17
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August 2, 2025
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Protein come out of the box but trjconv command didn't fix the problem
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10
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4207
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August 2, 2025
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I cannot follow the martini tutorial Parametrization of a new small molecule
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11
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361
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July 31, 2025
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Problem with gromacs script generetated with charmm-gui
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3
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29
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July 30, 2025
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Distance restrained in my protein amino acids with Zn ion present in it
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0
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9
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July 30, 2025
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High LJ (SR) in graphene sheet minimization
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0
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11
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July 28, 2025
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Pressure Scaling more than 1% and volume fluctuations
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1
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51
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July 25, 2025
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Using -membed option in gromacs
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3
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108
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July 25, 2025
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Query about pullf.xvg plot
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4
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44
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July 23, 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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31
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July 21, 2025
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How to create restrained file for sol
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0
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20
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July 15, 2025
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Membrane Protein ligand simulation
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11
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273
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July 10, 2025
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Restraining Solvent Molecules Under an Ice Slab
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0
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27
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July 6, 2025
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Segmentration Fault and to small of a timestep problem from a Amber built system
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19
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564
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November 11, 2024
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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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74% GPU utilization and 2/3 power usage on WSL2
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1
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34
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July 2, 2025
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Simulation with a 3 fs timestep
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0
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30
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June 30, 2025
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