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    1. Should I waste time compiling everything to run in parallel?
    2. Do I need to compile in double precision?

    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 I provide multiple definitions of bonds / dihedrals in a topology?
    4. Do I really need a .gro file?
    5. Do I always need to run pdb2gmx when I already produced an .itp file elsewhere (like PRODRG)?
    6. How can I build in missing atoms?
    7. Why is grompp -np broken under GROMACS 4?
    8. Why is the total charge of my system not an integer like it should be?

    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?
    7. How can I do a simulation at constant pH?
    8. How should I compute a single-point energy?

    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 visualize a trajectory?
    2. Why am I seeing bonds being created when I watch the trajectory?
    3. When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?
    4. Why is my total simulation time not an integer like it should be?
    5. How do I reduce the huge amount of data I have to store for my analysis?
    6. How do I automate interaction with GROMACS utilities for use in scripts?
    7. Why is my pressure fluctutating wildly?
    8. Why does my average structure look messed up?
    9. How do I make an index file for dihedral PCA?
    10. Why does do_dssp take so long when I ask it to run DSSP on every frame in my trajectory?
    11. Why doesn't g_energy do anything after I press Enter?
    Page last modified 00:43, 12 Jul 2012 by mabraham