FAQs

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Version as of 02:53, 10 Aug 2020

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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?

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