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A Custom Water Force Field Implementation
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0
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6
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October 17, 2025
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Modify residues using CHARMM-GUI pdb reader and manipulator
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0
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11
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October 14, 2025
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GROMACS 2025.3 CUDA 13 RTX 5070 Ti Fails on Simulations
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2
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32
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October 14, 2025
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Performance of SMD simulation
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1
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28
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October 10, 2025
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How to simulate a cyclic protein with AMBER99SB ff?
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1
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21
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October 9, 2025
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Tools for creating initial .gro and combining source files
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0
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13
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October 8, 2025
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what should do with zink-protein.pdf to get topology file?
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5
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40
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October 7, 2025
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Help: RTX 5080 (Blackwell, Compute Capability 12.1) + WSL2 + CUDA 13.0 “No Kernel Image Available”
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2
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81
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October 5, 2025
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Pdb2gmx fails: Residue 'MGP' not found in CHARMM36 force field
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2
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35
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October 5, 2025
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How to setup protein-ligand simulation using CHARMM-GUI for ligand preparation
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4
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39
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October 3, 2025
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How should I choose the box size for nanodisc simulations?
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1
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23
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October 3, 2025
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Hydrogen bonds increase with temperature in MD simulation – unexpected behavior
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4
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53
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October 3, 2025
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x2top for MINFF
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0
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19
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October 2, 2025
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ZINK in Protein
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2
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29
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October 1, 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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38
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September 29, 2025
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Question on Restraint Protocol During Staged Equilibration
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0
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13
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September 27, 2025
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gmx_ffconv: A Fast, User-Friendly Semi-Automated All-Atom Force Field Converter for GROMACS
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0
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55
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September 21, 2025
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Using H2O2 as a solvent for MD simulation
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3
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38
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September 19, 2025
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How to generate an .itp file for MoSSe
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0
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11
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September 17, 2025
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Reproducing TIP4P/2005 water properties
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10
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68
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September 15, 2025
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Placing the position restrained itp file of a ligand in protein-ligand topology file
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2
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20
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September 10, 2025
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RMSD graph after protein protein md simulation
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4
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69
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September 8, 2025
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Rigid TIP4P energy and force computations
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8
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38
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September 5, 2025
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Charm gui equilibration steps
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9
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70
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September 5, 2025
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Membrane artefacts when pulling membrane proteins together using Martini forcefield
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3
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24
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September 4, 2025
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Assistance Needed: "Atomtype F not found" Error in GROMACS Minimization with TFE Solvent
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1
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18
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September 3, 2025
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How do I correctly re-wrap DCLE tail-solvent and lipids in an HMMM trajectory?
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2
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20
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September 3, 2025
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How to generate topology and .itp files for succinic acid and Zn²⁺ in GROMACS using OPLS-AA?
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0
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20
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August 28, 2025
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NPT parameter
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0
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19
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August 27, 2025
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PBC correction for drug–lipid bilayer system (GROMACS 2024.5)
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0
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24
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August 19, 2025
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