I was looking for examples of calculation setups. So I have a couple of
questions about one used in this paper
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008
Parameters are amber99sb-ildn and gaff:
"Simulations were carried out with GROMACS [40,41], version 4.6. All
bonds were con-
strained using the P-LINCS algorithm [42], allowing an integration time
step of 2 fs. The Verlet
cutoff scheme [43] was used with a minimum cutoff of 1.0 nm for
short-range Lennard-Jones
interactions and the real-space contribution to the smooth Particle Mesh
Ewald algorithm
[44,45]"
Why all-bonds constraints are applied? Isn't AMBER FF are supposed to be
used with h-bond constraints? Is there any notable difference between 1
and 2fs timestep in this setup?
Is box-solute distance of 1.0nm sufficient for 1.0nm LJ cuttof?
And why run three independent 500ns simulations instead of one or two of
longer duration? Only to check for reproducibility or are there any
additional reasons?
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