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How create uneven box for all-atom simulation
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4
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65
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October 15, 2026
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Position restraints and mdp setup after an AmberTools(ZAFF) -> ParmEd -> GROMACS handover
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0
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43
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October 13, 2026
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Low GROMACS Performance on RTX 5090 Workstation
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4
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371
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August 31, 2026
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Tabulated function for 1-4 interactions
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1
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75
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August 25, 2026
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MDrun: Simulation speed jumping a factor of 10 with a gpu executable
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6
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107
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August 24, 2026
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Loss of performance in v. 2021
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27
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1969
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August 24, 2026
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"Accelerating molecular dynamics simulations using fast Ewald summation with prolates" paper
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6
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282
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August 13, 2026
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RTX 5070 Not Utilized
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3
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762
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August 1, 2026
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Multiple gmx processes on GPU(s) ran too slowly
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10
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245
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July 13, 2026
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Gromacs warning when calculating RMSD: excessively large distances exist or the system is exploding
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1
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47
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June 24, 2026
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Fatal Error: no domain decomposition for rank 4, min cell size 1.776 nm
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1
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55
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June 24, 2026
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WT vs mutant protein-protein complex MD: should mutant be generated from WT docked complex or redock
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0
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39
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June 15, 2026
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What if the protein contains mutations and missing residues?
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2
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139
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June 4, 2026
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Box changing shape after equilibration
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8
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200
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May 26, 2026
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How to solve inconsistent shifts over periodic boundaries in protein-dna run in minimization step?
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11
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3153
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May 17, 2026
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Segmentation fault without further information
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3
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106
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May 13, 2026
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Colvars: Error: keyword "customfunction" is not supported
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3
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216
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May 12, 2026
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LINCS Error in production run
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2
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175
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May 1, 2026
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Mdrun with awh for a dimeric protein
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0
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57
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April 29, 2026
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Energy calculations during mdrun with multiple groups
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2
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75
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April 23, 2026
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Extreme performance loss with version 2026.1 on APUs
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10
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248
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April 13, 2026
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GROMACS Command for Minimization, Equilibration, Production Runs from CHARMM README
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0
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68
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April 4, 2026
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Abnormal dVremain/dl values in GROMACS 2025.0 with vdw-type=pme and free-energy
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3
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51
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March 31, 2026
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Issues regarding MDrun in HPC
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0
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34
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March 26, 2026
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Coulomb (SR) calculation in PME
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9
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150
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March 19, 2026
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Steered Molecular dynamics of a ligand moving towards bilayer membrane
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1
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86
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March 16, 2026
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Paradoxical Density in OPLS-AA: Diesel mixture density is abnormally LOWER than its lightest compone
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6
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115
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March 15, 2026
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Restart MD run from a particular time moment in *.xtc file?
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5
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144
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March 6, 2026
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Gromacs-CP2k energy minimization
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0
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55
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February 24, 2026
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Steered MD Simulation error
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19
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383
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February 19, 2026
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