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Uniaxial Elongation to get tensile stress vs. tensile strain curve
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7
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122
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August 29, 2025
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Your Review on AMBER19sb MD in GROMACS2026
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1
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185
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February 4, 2026
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Adding [Fe4S4]+2 cluster parameters to charmm36.ff file
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2
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172
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August 5, 2025
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Large differences in gmx mindist values with and without PBC correction
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5
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100
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November 25, 2025
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Analyzing REMD trajectories to understand effect of temperature on protein structure
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1
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168
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October 1, 2025
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Hydrogen bond analysis in MD simulation
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2
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146
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October 26, 2025
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Maxwell distribution gen_t
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6
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96
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August 12, 2025
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Using H2O2 as a solvent for MD simulation
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3
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124
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September 19, 2025
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Problem in using make_ndx to define index
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5
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105
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February 13, 2026
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Error while analyzing .tpr file generated using gromacs 2025.2
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6
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98
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August 11, 2025
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How to build Ligand topology
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2
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145
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February 4, 2026
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PBC changing drastically vertical in replicas of membrane protein with plumed
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6
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92
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November 12, 2025
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Simulation with large number of particles
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4
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106
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September 4, 2025
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"Accelerating molecular dynamics simulations using fast Ewald summation with prolates" paper
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4
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125
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July 7, 2026
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Hydrogen bonds increase with temperature in MD simulation – unexpected behavior
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4
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120
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October 3, 2025
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How to set up protein–peptide complex simulation in GROMACS: peptide as ligand or whole complex?
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1
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172
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September 29, 2025
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Problem with gromacs script generetated with charmm-gui
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3
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114
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July 30, 2025
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Segfault with ntmpi >2 with 2 GPUs
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6
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85
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November 12, 2025
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Is it possible to extract coordinates from a .cpt file?
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4
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104
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December 15, 2025
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Protein glycan simulation
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4
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101
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November 23, 2025
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Comm-mode setting in applied field simulation in membrane-protein complex
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3
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132
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September 9, 2025
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Performance regression in 2025.4: suboptimal CUDA NBNxM kernel selection vs 2024.2
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7
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114
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February 12, 2026
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Gmx-mdmat-queries
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0
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44
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September 30, 2025
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Membrane protein for gmx_mmpbsa
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1
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184
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September 19, 2025
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GROMACS can't find files that are in the working directory
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3
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114
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November 14, 2025
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Membrane artefacts when pulling membrane proteins together using Martini forcefield
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3
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114
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September 4, 2025
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Slipids instead of CHARMM-GUI
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3
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104
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October 3, 2025
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Solvation Box Distance Default or Protein-specific?
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3
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105
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September 8, 2025
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21st January, GROMACS quarterly planning meeting 9:00 CET
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6
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121
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January 28, 2026
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HPC Software Scientist: GROMACS / Mixed Precision (KTH/PDC, Stockholm)
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0
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211
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November 19, 2025
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gmx g_rdf on parallel computer
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4
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98
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November 21, 2025
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The potential energy becomes positive after assigning partial charges
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4
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92
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November 18, 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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116
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December 3, 2025
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C-rescale vs Parrinello–Rahman in final NPT equilibration before protein–protein SMD (TCR–pMHC, ~1M
|
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1
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150
|
April 8, 2026
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Shear Viscosity Calculation for Isotropic Molecules
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7
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86
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June 9, 2026
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MDRun Losing Atoms
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7
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84
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February 10, 2026
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Problem installing gmxapi on Ubuntu
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5
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103
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March 13, 2026
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Energy minimization using only CPU (GPU not used) — GROMACS 2025.3 version used on Ubuntu
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1
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138
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September 15, 2025
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How to include bound calcium in amylase structure
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4
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88
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November 21, 2025
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The largest distance between excluded atoms is 7.247 nm, which is largerthan the cut-off distance. T
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1
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136
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September 30, 2025
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Core dumped error while production run
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5
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101
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September 27, 2025
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15th April, bi-weekly GROMACS meeting - morning edition
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2
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76
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April 14, 2026
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GROMACS 2025.3 + Plumed +GPU + MPI
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2
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129
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November 24, 2025
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How to generate topology file for a non-standard ligand file?
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1
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132
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September 12, 2025
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Statistical Analysis Method for Peak force and total work in Steered molecular dynamics
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3
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67
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June 4, 2026
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Questions regarding AWH and comparison to MBAR
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3
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111
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February 10, 2026
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Position restraints causing mdrun to stall on step 0
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3
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96
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November 17, 2025
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Query:Reagrding using the multiple nodes's GPU or CPU to run MD production step in gromacs
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4
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105
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November 20, 2025
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Restart MD run from a particular time moment in *.xtc file?
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5
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84
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March 6, 2026
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PBC effect on RMSD calculation
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2
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101
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October 1, 2025
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