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    1. Should I waste time compiling everything to run in parallel?

    System Preparation and Preprocessing

    1. Where can I find a TIP3P coordinate file for use with genbox?
    2. How do I get genbox not to put waters inside my micelle/membrane/protein?
    3. How do you provide multiple definitions of bonds / dihedrals in a topology?
    4. Do I really need a .gro file?
    5. Why am I mistakenly using pdb2gmx when I already obtained an .itp file from elsewhere (like PRODRG)?
    6. Why is grompp -np broken under GROMACS 4?

    Simulation Methodology

    1. Should I temperature-couple a handful of ions to their own thermal bath?
    2. Why do my grompp restarts always start from time zero?
    3. Why can't I do conjugate gradient minimization with constraints?
    4. Why can't I constrain atoms in place in my energy minimization or simulation?
    5. How do I extend a completed a simulation to longer times?
    6. How do I complete a crashed simulation?

    Parameterization and Force Fields

    1. 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?
    2. Should I take parameters from one force field and apply them inside another that is missing them?

    Analysis and Visualization

    1. How do I automate interaction with GROMACS utilities for use in scripts?
    2. How do I visualize a trajectory?
    3. Why is my pressure fluctutating wildly?
    4. Why does my average structure look messed up?
    5. How do I make an index file for dihedral PCA?
    6. Why am I seeing bonds being created?
    7. When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?
    8. How can I do a simulation at constant pH?
    9. Why does do_dssp take so long when I ask it to run DSSP on every frame in my trajectory?
    10. Why doesn't g_energy do anything after I press Enter?
    11. How do I reduce the huge amount of data I have to store for my analysis?
    12. How can I build in missing atoms?
    13. Why is my total simulation time or total charge not an integer like it should be?
    Page last modified 14:01, 21 Jun 2011 by JLemkul?