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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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33
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January 26, 2026
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How to add hydrogen atoms to the complex with correct coordinates?
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2
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21
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January 23, 2026
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Free energy verification by thermodynamic integration in liquid solutions
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0
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17
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January 22, 2026
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Segmentation faults / ‘core dumped’ errors
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12
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58
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January 22, 2026
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The output average of gmx energy differs from the average of the data stored in .xvg
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3
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15
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January 22, 2026
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DSSP stuck
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0
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12
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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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21
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January 21, 2026
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Pdb2gmx rounds up the charge of a single atom
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7
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40
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January 21, 2026
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Charge precision in topology files: parsing behaviour and validation tolerance
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5
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45
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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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42
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January 21, 2026
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Water box elongation
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1
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25
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January 21, 2026
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Post MD simulation Visualizations
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2
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66
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January 15, 2026
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Gromacs .hdb format RU5 case study
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3
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20
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January 14, 2026
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Slow simulation
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3
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49
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January 12, 2026
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Npt vs nvt
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1
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34
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January 11, 2026
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COF molecular dynamics simulation model creation
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1
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72
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January 10, 2026
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All atom membrane
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0
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24
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January 9, 2026
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Protein ns MD simulation and other times recommended inquiry?
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21
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386
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January 8, 2026
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Installation of GROMACS on a intel Arc A750 GPUs
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2
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27
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January 8, 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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31
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January 7, 2026
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Is it possible to add other form of lennard jones potential form (such as LJ9-3, LJ6-3) in gromacs?
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3
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43
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January 7, 2026
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Fatal error: number of coordinates in coordinate file does not match topology file
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7
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1741
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January 7, 2026
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Steered MD Simulation using Gromacs
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2
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46
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January 7, 2026
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Does GROMACS distinguish Rp/Sp chiral phosphate modifications at O1P vs O2P in DNA?
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0
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13
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January 5, 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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27
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January 5, 2026
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Non-integer total charge after partial charge replacement for a covalent Cys–maleimide patch
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0
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29
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December 31, 2025
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Colvars' distancePairs to get minimum distance between molecules
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1
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22
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December 30, 2025
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Installation error, missing libcufft.so.10
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2
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368
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December 29, 2025
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Should I manually set -ntomp 16 or let Gromacs auto-configure its settings？
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4
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70
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December 29, 2025
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