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Pull code (umbrella, distance): Fatal error "Pull reference distance … needs to be non-negative"
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1
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29
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February 11, 2026
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MDRun Losing Atoms
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7
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54
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February 10, 2026
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SMD simulation - protein pulling and resulting rotation
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2
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38
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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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48
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February 10, 2026
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GROMACS conda version that uses AVX_512 with GPU
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14
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77
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February 10, 2026
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Amber99sb-ildn ff with Hydroxyproline
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1
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43
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February 10, 2026
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Ligand mlecule containing boron atom
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1
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33
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February 10, 2026
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Proteolytic cleavage of aggregate protein by enzyme
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3
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33
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February 9, 2026
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Pdb2gmx fails to recognize OXT in terminal valine
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1
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33
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February 7, 2026
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Workstation options
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1
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26
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February 5, 2026
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How to build Ligand topology
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2
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63
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February 4, 2026
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no default bond types, angle types or dihedral types
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1
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22
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February 4, 2026
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PBC issues when simulating multimeric assembly
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1
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31
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February 4, 2026
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Instantaneous positional shifts of protein trajectory
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1
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15
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February 4, 2026
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PBC centering Issue
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1
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33
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February 4, 2026
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[Errors] Problems during Umbrella Sampling
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1
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28
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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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71
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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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41
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February 4, 2026
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Simulated annealing of protein-DNA complex
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0
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32
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February 3, 2026
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SAM co-factor with CHARMM force field for GROMACS silmualtion
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10
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246
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February 3, 2026
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Gmx filter
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26
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224
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February 2, 2026
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Why not protein is not come in the selection
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1
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10
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January 31, 2026
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Question about how LINCS calculates stress
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5
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50
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January 30, 2026
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Umbrella sampling for a protien ligand system
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1
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31
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January 29, 2026
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Error problem
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1
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18
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January 29, 2026
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Absolute FEP result too high
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2
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34
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January 29, 2026
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MPI error when using ensemble-averaged distance restraints and set GMX_DISRE_ENSEMBLE_SIZE
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10
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67
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January 27, 2026
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Is is good to simulate lipid bilayer with NVE ensemble
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0
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24
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January 26, 2026
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Pdb2gmx handling altlocs
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1
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12
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January 26, 2026
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Struggling to replicate free energy calculations in pmx tutorial using FEP
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0
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40
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January 26, 2026
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