Gromacs

FAQs

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    Version as of 08:38, 20 Oct 2019

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    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. Should I temperature-couple a handful of ions to their own thermal bath?
    5. Why does my average structure look messed up?
    6. Where can I find a TIP3P coordinate file for use with genbox?
    7. How do I make an index file for dihedral PCA?
    8. How do I get genbox not to put waters inside my micelle/membrane/protein?
    9. Why am I seeing bonds being created?
    10. 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?
    11. When visualizing a trajectory from a simulation using PBC, why are there holes or my peptide leaving the simulation box?
    12. How can I do a simulation at constant pH?
    13. Why does do_dssp take so long when I ask it to run DSSP on every frame in my trajectory?
    14. How do you provide multiple definitions of bonds / dihedrals in a topology?
    15. Why doesn't g_energy do anything after I press Enter?
    16. Why do my grompp restarts always start from time zero?
    17. How do I reduce the huge amount of data I have to store for my analysis?
    18. Do I really need a .gro file?
    19. Why am I mistakenly using pdb2gmx when I already obtained an .itp file from elsewhere (like PRODRG)?
    20. Why can't I do conjugate gradient minimization with constraints?
    21. Why can't I constrain atoms in place in my energy minimization or simulation?
    22. Should I waste time compiling everything to run in parallel?
    23. Should I take parameters from one force field and apply them inside another that is missing them?
    24. Why is grompp -np broken under GROMACS 4?
    25. How do I extend a completed a simulation to longer times?
    26. How do I complete a crashed simulation?
    27. How can I build in missing atoms?
    28. Why is my total simulation time or total charge not an integer like it should be?
    Page last modified 03:29, 7 Dec 2010 by mabraham