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Running gmx_mmpbsa for protein receptor - homodimer protein complex
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0
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62
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August 18, 2026
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How to use machine learning potential trained by deepmd-kit in Gromacs?
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1
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104
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August 17, 2026
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Segmentation fault during slow SMD pulling through a constricted pore
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7
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108
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August 12, 2026
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PBC-related jumps in protein–protein contact analysis of a Martini CG simulation
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0
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43
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August 12, 2026
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Topology and force-field parameters for Rhodamine B in water
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0
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63
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August 10, 2026
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Use of the CRYST1 values in the DSSP calculation
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8
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147
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August 10, 2026
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Terminates abruptly /crashes
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1
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59
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August 10, 2026
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C-rescale barostat and simulated annealing
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4
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119
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August 6, 2026
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Issue generating PFBS anion parameters with LigParGen
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2
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120
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August 5, 2026
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Z‑dimension of the box decreases
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3
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94
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August 5, 2026
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HEAVY_H masses in the CHARMM36m GROMACS force field
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9
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199
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August 5, 2026
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Constructing core shell nanoparticle
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0
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46
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August 4, 2026
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Extend option in gmx convert-tpr
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12
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6169
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August 3, 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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Correct protocol for generating independent replicas of a membrane-protein simulation.
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3
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120
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July 30, 2026
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Advice on CGenFF penalty scores for a large, DFT-optimised molecule
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4
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140
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July 29, 2026
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Preprocessing error with CGenFF 5.0 topology: unsupported multiple CHARMM type-9 dihedral parameters
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0
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31
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July 29, 2026
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How create Charmm36 topology parameters for glycans
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2
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80
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July 28, 2026
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Parametrization of pyroglutamate
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2
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79
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July 28, 2026
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AWH convergence for a charged ligand permeating a bilayer
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5
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115
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July 28, 2026
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Trans to cis confirmation at NVT step
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0
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33
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July 28, 2026
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Regressiontests/complex tests fail with intelmpi GHROMACS build
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1
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58
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July 27, 2026
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How to simulate EDLC (Electrochemical Double Layer)?
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1
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175
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July 24, 2026
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Simulation of a dizinc metallo protein
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6
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619
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July 24, 2026
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When is trajectory preprocessing (whole/cluster/nojump/center) actually required for analysis?
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2
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118
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July 24, 2026
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Umbrella sampling simulation pulling towards periodic box using martini 3 forcefield
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3
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77
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July 23, 2026
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X2top not generating listed interactions correctly
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1
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69
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July 23, 2026
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Simulating an Infinite polymer across boundaries
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1
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65
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July 23, 2026
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"No default Per. Imp. Dih. types" when using amber14sb_parmbsc1_cufix force field
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0
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38
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July 21, 2026
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How to remove duplicate frames
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2
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66
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July 20, 2026
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