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Issue with Running GROMACS on a Protein Containing ATP
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4
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30
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September 4, 2024
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Can I simulate 2 proteins and 1 ligand?
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2
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34
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March 13, 2025
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How to Confirm if SETTLE Algorithm is Applied in TIP4P Water Model Simulation?
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2
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44
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February 4, 2025
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Running simultaneous jobs in a same machine
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2
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40
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January 26, 2025
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Gmx traj looks weird
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2
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40
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November 1, 2024
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Pull simulation error: Umbrella sampling simulation of peptide and lipid system (MARITNI CG)
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2
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38
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October 30, 2024
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Structure appear broken
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2
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36
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September 16, 2024
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Signalling bug in gro file writer
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2
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35
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September 9, 2024
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25th June, biweekly GROMACS developer meeting - afternoon edition
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1
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45
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June 25, 2025
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Error during Gromacs-cp2k install
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1
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47
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February 12, 2025
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Check the Forcefield of the electrolyte system EC DEC DMC
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1
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45
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September 9, 2024
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Post-doctoral positions Campinas/Brazil (UNICAMP)
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0
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73
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May 30, 2025
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One or more water molecules cannot be settled during energy minimization
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0
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57
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October 21, 2024
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Ionic conductivity using Green-Kubo formulation
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0
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57
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September 24, 2024
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Atom C1 not found in building block 1MET while combining tbp and trp
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0
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54
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May 18, 2025
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Problems building gromacs with CUDA
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0
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55
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April 29, 2025
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PCA and FEL for mutated structures in Gromacs
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0
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60
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January 3, 2025
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Gromacs setup
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0
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56
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December 10, 2024
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Box size decreasing during production run?
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3
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29
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October 22, 2024
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Topology mismatch
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3
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29
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September 18, 2024
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Segmentation fault with REMD+GPU--potential bug?
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5
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32
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April 11, 2025
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Help centering, fitting, and analysis on a protein that contains a chain of D-residues
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1
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39
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February 3, 2025
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Gmx msd standard library logic error
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1
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43
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January 18, 2025
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August 21st, biweekly GROMACS developer meeting
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1
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50
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August 21, 2024
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30th April - biweekly GROMACS developer meeting - afternoon edition
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2
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46
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April 30, 2025
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Remove Coulomb interaction
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2
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47
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March 4, 2025
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Box Size Expansion and Gaps between Periodic Images in NPT Simulation
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2
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48
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February 27, 2025
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Dehydrated bilayer simulation
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2
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35
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January 30, 2025
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DNA Backbone Parametrization and rtp File
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1
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52
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January 20, 2025
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Error in residue topology database
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1
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39
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December 19, 2024
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Fatal error: Index[9411] 92818 is larger than the number of atoms in the trajectory file (9591)
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1
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38
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October 28, 2024
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Non-standard amino acid alchemical mutation - dihedrals error
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1
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43
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September 25, 2024
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Fatal error: Perturbed masses or constraints are not supported by rerun
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1
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43
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September 10, 2024
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Removing Outlier Residues in RMSD and RMSF Calculations - GROMACS
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1
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39
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August 22, 2024
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Degrees of freedom
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3
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30
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June 11, 2025
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How to prevent two molecules from interacting with each other?
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3
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37
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April 4, 2025
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How do I convert the parameters of Buckingham potential to the parameters of LJ
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0
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60
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December 2, 2024
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Crystal water molecules occupying a strange position
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3
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39
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November 2, 2024
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Gmx distance
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2
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36
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November 8, 2024
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Constrained dynamics of oxygen atoms of water molecules
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2
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44
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October 21, 2024
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Free energy of specific bond breaking/formation through thermodynamic integration
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4
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33
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November 12, 2024
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The cumulative heat exchanged between the simulation system and thermal bath
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4
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35
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September 26, 2024
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How to calculate water density after removing PBC?
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4
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27
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September 17, 2024
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Charged solute, thermodynamic integration, couple-intramol = yes
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0
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69
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September 1, 2024
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Gmx current
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0
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54
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August 7, 2024
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HIS Protonation Assignment using pdb2gmx
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1
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42
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April 9, 2025
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Error in user input: Invalid input values Required option was not provided
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1
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38
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January 10, 2025
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Error in making protein topology
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1
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37
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September 24, 2024
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Gromacs and cuFFT
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6
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32
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July 31, 2025
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Issue while extracting pdb from trajectory
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2
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36
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January 22, 2025
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