Table of contents
No headers - How do I automate interaction with GROMACS utilities for use in scripts?
- How do I visualize a trajectory?
- Why is my pressure fluctutating wildly?
- Should I temperature-couple a handful of ions to their own thermal bath?
- Why does my average structure look messed up?
- Where can I find a TIP3P coordinate file for use with genbox?
- How do I make an index file for dihedral PCA?
- How do I get genbox not to put waters inside my micelle/membrane/protein?
- Why am I seeing bonds being created?
- I want to simulate a molecule (protein, DNA, etc.) which complexes with various transition metal ions, iron-sulfur clusters, or other exotic species. Parameters for these exotic species aren't available in force field X. What should I do?
- When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?
- How can I do a simulation at constant pH?
- Why does do_dssp take so long when I ask it to run DSSP on every frame in my trajectory?
- How do you provide multiple definitions of bonds / dihedrals in a topology?
- Why doesn't g_energy do anything after I press Enter?
- Why do my grompp restarts always start from time zero?
- How do I reduce the huge amount of data I have to store for my analysis?
- Do I really need a .gro file?
- Why am I mistakenly using pdb2gmx when I already obtained an .itp file from elsewhere (like PRODRG)?
- Why can't I do conjugate gradient minimization with constraints?
- Why can't I constrain atoms in place in my energy minimization or simulation?
- Should I waste time compiling everything to run in parallel?
- Should I take parameters from one force field and apply them inside another that is missing them?
- Why is
grompp -np
broken under GROMACS 4? - How do I extend a completed a simulation to longer times?
- How do I complete a crashed simulation?
- How can I build in missing atoms?
- Why is my total simulation time or total charge not an integer like it should be?
- Where is the missing TIP3P water box for doing solvation?