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How create uneven box for all-atom simulation
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4
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30
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October 15, 2026
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Position restraints and mdp setup after an AmberTools(ZAFF) -> ParmEd -> GROMACS handover
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0
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27
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October 13, 2026
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Mdp file differences between CHARMM27 and CHARMM36 parameters
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4
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87
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October 7, 2026
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Chloroform as a solvent in Charmm36 force field
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3
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284
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October 5, 2026
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How to generate a GROMACS topology (.itp) for a silver nanocluster using the INTERFACE Force Field?
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0
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36
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September 30, 2026
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Port LignAmb25 Force Field to GROMACS
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3
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136
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September 10, 2026
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NPγT vs NPT for Unrestrained Membrane Equilibration Using the CHARMM36 Force Field
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10
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200
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August 26, 2026
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Query on electrostatic treatment for slab/interface systems (2D periodicity)
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1
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49
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August 24, 2026
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Discontinuity in bias energy function for periodic collective variables
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4
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92
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August 20, 2026
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Topology and force-field parameters for Rhodamine B in water
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0
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62
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August 10, 2026
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Issue generating PFBS anion parameters with LigParGen
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2
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117
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August 5, 2026
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HEAVY_H masses in the CHARMM36m GROMACS force field
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9
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182
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August 5, 2026
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Constructing core shell nanoparticle
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0
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45
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August 4, 2026
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Parametrization of pyroglutamate
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2
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73
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July 28, 2026
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Simulation of a dizinc metallo protein
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6
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606
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July 24, 2026
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X2top not generating listed interactions correctly
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1
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55
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July 23, 2026
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How to determine b0 and kb in Zn-coordinated bond
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0
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42
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July 2, 2026
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IFT in CG simulation using MARTINI 3.0
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1
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63
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June 12, 2026
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Modified dihedral notation
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6
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118
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June 3, 2026
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0
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81
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April 26, 2026
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Covalent bound PLP to SPT (membrane bound)
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0
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56
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April 22, 2026
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Obtaining parameters for ligands in a nanoparticle assembly
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0
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52
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April 5, 2026
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0
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27
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April 1, 2026
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PEG2000 collapsing into bilayer core in atomistic simulation (GROMOS 53A6)
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0
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38
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March 19, 2026
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Amber FF parameters for metal binding centres
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4
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1469
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March 17, 2026
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Newest CHARMM36 port for GROMACS
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39
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26174
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March 5, 2026
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Amber19SB and Amber14SB in old versions of Gromacs
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13
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733
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February 27, 2026
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Define ATP+mg in Amber forcefield
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0
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65
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February 23, 2026
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CGenFF ERROR - attype warning: unknown sulfur type (SD) not supported; skipped molecule
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2
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354
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February 16, 2026
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Amber99sb-ildn ff with Hydroxyproline
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1
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71
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February 10, 2026
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