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Differences in the implementation of 1-4 interactions
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4
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564
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March 19, 2024
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Creating topology for chimeric DNA/RNA strand
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0
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72
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March 19, 2024
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Gmx pdb2gmx
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1
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61
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March 18, 2024
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Cannot find the force fields that I put in a directory, working_dir/charmm36.ff
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4
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77
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March 16, 2024
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Calculating the system temperature from the velocity information from .gro file
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4
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92
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March 15, 2024
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Extrapolating LJ14 and Coul 14 entries from LJ (SR) and Coul (SR) when [ pairs_nb ] is used
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0
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58
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March 15, 2024
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GROMOS96 43a1 force field for ligand topology
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10
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82
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March 14, 2024
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Coarse-grained md simulatioin
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2
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75
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March 14, 2024
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How to use brownian dynamics with gromacs
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2
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86
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March 12, 2024
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ImportError: cannot import name 'gcd' from 'fractions'
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7
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3094
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March 12, 2024
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`No default Improper Dih. types` for ACE-PRO-NME peptide with charmm36-jul2022.ff
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1
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60
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March 10, 2024
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Parameterization of an adenylylated tyrosine residue in CHARMM36
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0
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63
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March 7, 2024
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Problem in creating Topology by command pdb2gmx
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3
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76
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March 6, 2024
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Blow up during NPT equilibration using Berendsen barostat
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3
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122
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March 6, 2024
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Error in generating ligand topology using CGenFF and python 3.9
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1
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60
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March 6, 2024
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CG-CD1 TRP bond oscillational less than 0.004 fs
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1
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86
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March 6, 2024
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Problem with acetylated and amidated termini in pdb2gmx command
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1
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401
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March 6, 2024
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Molecular dynamic simulation of alkaloids
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0
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81
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March 2, 2024
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Create Ligand topology file
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11
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4405
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March 2, 2024
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DNA-RNA Simulations
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7
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199
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March 1, 2024
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Does maximum time step for a system depend on equilibration state, or only on topology?
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2
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138
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February 29, 2024
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Preparation of Ligand.itp file for a Iron metal coordination complex
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2
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96
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February 29, 2024
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Gmx_MMPBSA binding energy
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6
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181
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February 29, 2024
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Error: Residue ' ' not found in residue topology database
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1
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132
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February 26, 2024
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Electrostatic force between virtual interaction sites
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1
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67
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February 25, 2024
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How to handle phospho-serine residues in protein structures for Martini coarse-grained simulation?
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0
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48
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February 22, 2024
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PACKMOL and gmx2pdb
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0
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102
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February 20, 2024
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CHARMM parameterization destroys ligand structure
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0
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98
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February 19, 2024
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Correcting the pdb file manually
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0
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80
|
February 19, 2024
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Inserting a modified residue into a protein/DNA chain using pdb2gmx
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18
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771
|
February 17, 2024
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