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PBC Box Failing to Expand to Input .gro File Parameters + Unwanted Position Restrained Protein
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3
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82
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September 2, 2026
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NPγT vs NPT for Unrestrained Membrane Equilibration Using the CHARMM36 Force Field
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10
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159
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August 26, 2026
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CUDA illegal memory access during NPT equilibration
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9
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112
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August 21, 2026
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C-rescale barostat and simulated annealing
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4
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90
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August 6, 2026
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Z‑dimension of the box decreases
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3
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85
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August 5, 2026
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Trans to cis confirmation at NVT step
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0
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31
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July 28, 2026
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How many nanoseconds do I need to capture potential unbinding events for protein-protein interaction
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1
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80
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July 4, 2026
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Deform by Gromacs to apply shear rate
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8
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2646
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June 9, 2026
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COM motion removal during NVT simulation with electric field
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5
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134
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May 19, 2026
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Mdrun with awh for a dimeric protein
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0
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46
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April 29, 2026
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GROMACS SMD for TCR–pMHC: should TCR be pull group 1 or 2
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0
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44
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April 25, 2026
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Using AWH for bilayer permeability
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18
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1465
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April 22, 2026
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Changes of default `nstpcouple` and `nsttcouple` from version 2022 to 2023
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35
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2638
|
April 14, 2026
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C-rescale vs Parrinello–Rahman in final NPT equilibration before protein–protein SMD (TCR–pMHC, ~1M
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1
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209
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April 8, 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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41
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March 31, 2026
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Coulomb (SR) calculation in PME
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9
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129
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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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79
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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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94
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March 15, 2026
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Hydrogen mass repartitioning + multiple time step
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2
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79
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March 7, 2026
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ERROR 1 rvdw-switch must be < rvdw INQUIRY?
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4
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80
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March 5, 2026
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Steered MD Simulation error
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19
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323
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February 19, 2026
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Discrete "Coulp.-recip" values for different conformations of the same system
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10
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117
|
February 18, 2026
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Equilibration not work
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0
|
36
|
February 17, 2026
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SMD simulation - protein pulling and resulting rotation
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2
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121
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February 10, 2026
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Questions regarding AWH and comparison to MBAR
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3
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144
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February 10, 2026
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[Errors] Problems during Umbrella Sampling
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1
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71
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February 4, 2026
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Your Review on AMBER19sb MD in GROMACS2026
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1
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222
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February 4, 2026
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The contradiction between the mdp settings and the real pull rate
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13
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169
|
February 4, 2026
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Simulated annealing of protein-DNA complex
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0
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109
|
February 3, 2026
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Free energy verification by thermodynamic integration in liquid solutions
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0
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72
|
January 22, 2026
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