unanswered Martini 3: Recommended Simulation Parameters

  • Luke Kruse
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2 years 6 months ago - 2 years 6 months ago #9242 by Luke Kruse
Hello Everyone,

I am having a hard time digesting the following excerpt from the Martini 3 publication and was hoping that you could help me out.

General setup for CG molecular dynamics simulations and analysis

Settings for the CG simulations followed, in general, the ‘new’ Martini set of simulation parameters... For the Lennard-Jones terms, we used a cutoff scheme with a value of 1.1 nm and the Verlet cutoff scheme for the potential-shift. Long range electrostatic interactions were treated with reaction field or particle mesh Ewald, with relative permittivity set to εr = 15 and a cutoff value of 1.1 nm. Reaction field was used for most of the systems, except the ones explicitly mentioning particle mesh Ewald.

My questions are
  1. In the sentence beginning with "For the Lennard-Jones terms..." does this mean that the cutoff radius used in the development of the Martini3 FF parameters for the LJ interactions is shifted in such a fashion so that the value of the LJ interaction between a pair of atoms is zero at and beyond that separation distance, as well as a discontinuity in the force at that cut-off?
  2. If so, why was this approach taken instead of the gromacs "force-shift" method used previously (vdwtype=Cut-off with vdw-modifier=Force-switch)?
  3. I am a bit confused with how the electrostatic interactions are treated. From my understanding, the research paper suggests the "long range electrostatic interactions were treated with reaction field" but from reading the gromacs documentation on coulombic interactions with reaction field , it seems that the coulombic interactions are cut-off at a certain distance, as opposed to handling them with some sort of Ewald summation. Are these interactions indeed neglected beyond a certain cutoff distance?
  4. For the electrostatic interactions, was there a good reason to use values other than those provided by the Martini3 publication in a production run in a recent tutorial ? What is a good way to determine εr  and εrf ? Traditionally, I have seen the relative permittivity of water taken to be 80, but in the publication it poses 15, and here 1!

    The values they provided are reproduced here,
    nstlist                  = 5
    ns-type                  = Grid
    pbc                      = xyz
    rlist                    = 0.9
    coulombtype              = Reaction-Field
    rcoulomb                 = 1.4
    epsilon_rf               = 54
    epsilon_r                = 1
    vdw-type                 = Cut-off
    rvdw                     = 1.4

  5. What is also odd about the parameters used in this tutorial is that the neighbor list cutoff (rlist) is shorter than the van der Waals and coulombic cutoffs, which seems to suggest strange behavior for particles separated by r~rlist as whether or not the force is calculated for that pair is contingent upon whether they happened to be within rlist at the step the neighbor list was produced.

  6. Can you recommend good values to use for these parameters (εr , εrf, rcoulomb , etc. )?

Thank you all for your time,
Last edit: 2 years 6 months ago by Luke Kruse. Reason: Clarification of Question

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