Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Small ionic radii limit time step in Martini 3 molecular dynamics
  simulations   Among other improvements, the Martini 3 coarse-grained force field provides a
more accurate description of the solvation of protein pockets and channels
through the consistent use of various bead types and sizes. Here, we show that
the representation of Na$^+$ and Cl$^-$ ions as "tiny" (TQ5) beads limits the
accessible time step to 25 fs. By contrast, with Martini 2, time steps of 30-40
fs were possible for lipid bilayer systems without proteins. This limitation is
relevant for, e.g., phase separating lipid mixtures that require long
equilibration times. We derive a quantitative kinetic model of time-integration
instabilities in molecular dynamics (MD) as a function of time step, ion
concentration and mass, system size, and simulation time. With this model, we
demonstrate that ion-water interactions are the main source of instability at
physiological conditions, followed closely by ion-ion interactions. We show
that increasing the ionic masses makes it possible to use time steps up to 40
fs with minimal impact on static equilibrium properties and on dynamical
quantities such as lipid and ion diffusion coefficients. Increasing the size of
the bead representing the ions (and thus changing their hydration) also permits
longer time steps. The use of larger time steps in Martini 3 simulations
results in a more efficient exploration of configuration space. The kinetic
model of MD simulation crashes can be used to determine the maximum allowed
time step whenever sampling efficiency is critical.

0
The categories of this paper are: hep-ph
1
The categories of this paper are: cs
12
The categories of this paper are: nucl-th
25
The categories of this paper are: patt-sol
11
The categories of this paper are: hep-lat
16
The categories of this paper are: stat
17
The categories of this paper are: q-fin
8
The categories of this paper are: hep-ex
23
The categories of this paper are: solv-int
33
The categories of this paper are: plasm-ph
6
The categories of this paper are: astro-ph
7
The categories of this paper are: hep-th
20
The categories of this paper are: acc-phys
35
The categories of this paper are: mtrl-th
24
The categories of this paper are: dg-ga
10
The categories of this paper are: q-bio