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How to Apply Flat-Bottom Potential to a Specific Chloride Ion During Umbrella Sampling
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1
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19
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June 23, 2025
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NOTE 1 [file NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
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5
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1530
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June 23, 2025
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How to produce topology files for Platinum added metal complex?
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0
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12
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June 21, 2025
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Too many LINCS Warnings on coarse-grained polymer NPT run
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0
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15
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June 21, 2025
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Help setting annealing in nvt.mdp for polymer MD
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0
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14
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June 20, 2025
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Force field for MoS2
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1
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25
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June 20, 2025
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RMSD high fluctuation
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1
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13
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June 20, 2025
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LINCS Warning or Freeze Behavior Depends on GROMACS Version
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0
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15
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June 20, 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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381
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June 20, 2025
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Silicon Nitride simulation in triclinic box
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1
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16
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June 19, 2025
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Unexpected geometry change when combing `freezegrps` with `constraints` and running MD
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6
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33
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June 19, 2025
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NPT Equilibration error
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0
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19
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June 19, 2025
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Tip3p.gro download
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6
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84
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June 19, 2025
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Membrane protein simulation
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1
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22
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June 18, 2025
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How to write the trajectory file using center of mass of each molecule?
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4
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18
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June 18, 2025
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Water surface tension
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8
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53
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June 18, 2025
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Prepare HEME topology
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5
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530
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June 17, 2025
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There are inconsistent shifts over periodic boundaries in a molecule type
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14
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61
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June 16, 2025
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Reimaging GPCR trajectory
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2
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11
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June 13, 2025
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System is distroted on applying dc electric filed
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13
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65
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June 13, 2025
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Installation of gromacs w/ CUDA & MPI
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2
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1317
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June 13, 2025
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cuFFTMp + MPI with GROMACS 2025.2 on NVIDIA DGXA100
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0
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20
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June 12, 2025
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Workflow for incorporating a modified residue into a protein through CHARMM-GUI
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0
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9
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June 12, 2025
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Box re-sizing After running the md simulation
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5
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26
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June 12, 2025
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Illegal memory access
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2
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18
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June 12, 2025
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Exact control over kinetic energy by manual velocity setting
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0
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9
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June 12, 2025
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Choose proper awh1-dim1-force-constant and -diffusion in AWH
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6
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42
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June 11, 2025
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Ligand atoms miss matched after extract from protein ligand complex
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0
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9
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June 11, 2025
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Degrees of freedom
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3
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29
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June 11, 2025
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Semi-automated force field conversion within Gromacs: Looking for test systems/ beta testers
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0
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28
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June 9, 2025
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