Gromacs

FAQs

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    Version as of 00:26, 25 Aug 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?
    29. Where is the missing TIP3P water box for doing solvation?
    Page last modified 03:17, 19 Jun 2011 by mabraham