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Coulomb (SR) calculation in PME
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9
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44
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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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23
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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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22
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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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24
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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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20
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March 5, 2026
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Steered MD Simulation error
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19
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120
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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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45
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February 18, 2026
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Equilibration not work
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0
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21
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February 17, 2026
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SMD simulation - protein pulling and resulting rotation
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2
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41
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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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53
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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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30
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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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88
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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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42
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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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35
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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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20
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January 22, 2026
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Tabulated nonbonded potentials in GROMACS 2026
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1
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38
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January 21, 2026
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Comparing Simulations with Different Thermo/Barostats
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2
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48
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January 21, 2026
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Water box elongation
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1
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26
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January 21, 2026
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Conducting MD simulation on a zinc metalloprotein with 4 zinc ions
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0
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34
|
January 7, 2026
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Steered MD Simulation using Gromacs
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2
|
58
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January 7, 2026
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High pressure in x and y axis in a buble in a nano channel
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2
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29
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January 5, 2026
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Steered molecular dynamics - umbrella samling
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1
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68
|
December 8, 2025
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electric filed with position restraint
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0
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31
|
December 3, 2025
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Free energy peturbation mdp file settings for solvation free energy calculation
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3
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71
|
December 3, 2025
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Simulating a Reverse Transcriptase complex with RNA, DNA
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1
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41
|
December 1, 2025
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Box explodes using NPT.mdp
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2
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83
|
November 26, 2025
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Query regarding making all .mdp files for ionization, equllibration, energy minimization
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2
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43
|
November 25, 2025
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Position restraints causing mdrun to stall on step 0
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3
|
72
|
November 17, 2025
|
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How does hydrogen mass repartitioning with an increased time step of 4 fs affect other mdp options?
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16
|
1286
|
November 6, 2025
|
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Free-energy on virtual sites only (or vice versa)
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2
|
65
|
October 29, 2025
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