|
Best practice for using newer AMBER force fields (ff19SB) in GROMACS?
|
|
2
|
26
|
November 19, 2025
|
|
Adding missing dihedral interactions to a Force Field
|
|
1
|
35
|
October 31, 2025
|
|
How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
|
|
9
|
111
|
October 26, 2025
|
|
A Custom Water Force Field Implementation
|
|
0
|
27
|
October 17, 2025
|
|
Modify residues using CHARMM-GUI pdb reader and manipulator
|
|
0
|
26
|
October 14, 2025
|
|
Using PMX for ΔΔG on a glycosylated Fc (P238D back-mutation; PDB 3WJJ): viable workflows?
|
|
0
|
12
|
October 12, 2025
|
|
How to simulate a cyclic protein with AMBER99SB ff?
|
|
1
|
25
|
October 9, 2025
|
|
Tools for creating initial .gro and combining source files
|
|
0
|
17
|
October 8, 2025
|
|
what should do with zink-protein.pdf to get topology file?
|
|
5
|
45
|
October 7, 2025
|
|
Requesting for claud computing system for md production
|
|
2
|
34
|
October 7, 2025
|
|
mRNA forcefields issue
|
|
0
|
32
|
October 5, 2025
|
|
Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
|
|
2
|
41
|
October 5, 2025
|
|
Inaccurate thermostatting when simulating MD water
|
|
1
|
58
|
October 4, 2025
|
|
x2top for MINFF
|
|
0
|
32
|
October 2, 2025
|
|
How to set up protein–peptide complex simulation in GROMACS: peptide as ligand or whole complex?
|
|
1
|
56
|
September 29, 2025
|
|
Amber04 forcefield check in gromacs
|
|
1
|
40
|
September 23, 2025
|
|
gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS
|
|
0
|
77
|
September 21, 2025
|
|
How to generate an .itp file for MoSSe
|
|
0
|
12
|
September 17, 2025
|
|
Issue generating PFBS anion parameters with LigParGen
|
|
1
|
22
|
September 15, 2025
|
|
SARS-CoV-2 RNA simulation
|
|
0
|
20
|
September 8, 2025
|
|
Rigid TIP4P energy and force computations
|
|
8
|
44
|
September 5, 2025
|
|
Assistance Needed: "Atomtype F not found" Error in GROMACS Minimization with TFE Solvent
|
|
1
|
25
|
September 3, 2025
|
|
How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
|
|
0
|
26
|
August 28, 2025
|
|
`No default Improper Dih. types` for ACE-PRO-NME peptide with charmm36-jul2022.ff
|
|
6
|
201
|
August 18, 2025
|
|
Ligand Topology can't generated
|
|
2
|
34
|
August 7, 2025
|
|
ImportError: cannot import name 'gcd' from 'fractions'
|
|
10
|
4769
|
August 7, 2025
|
|
Adding [Fe4S4]+2 cluster parameters to charmm36.ff file
|
|
2
|
55
|
August 5, 2025
|
|
Why Does GROMACS Rename a DG Terminus to DG5 Without Manual Patching?
|
|
0
|
19
|
July 22, 2025
|
|
Homocysteine covalently bonded with a protein MD simulation how to perform
|
|
0
|
37
|
July 21, 2025
|
|
How to add GAFF force field to gromcs?
|
|
4
|
2819
|
July 18, 2025
|