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+ +
+

fix mscg command

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+

Syntax

+
fix ID group-ID mscg N keyword args ...
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+
+
    +

  • ID, group-ID are documented in fix command

    +
    • +

  • mscg = style name of this fix command

    +
    • +

  • N = envoke this fix every this many timesteps

    +
    • +

  • zero or more keyword/value pairs may be appended

    +
    • +

  • keyword = range or name or max

    +
    +range arg = on or off
+  on = range finding functionality is performed
+  off = force matching functionality is performed
+name args = name1 ... nameN
+  name1,...,nameN = string names for each atom type (1-Ntype)
+max args = maxb maxa maxd
+  maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom
+
    +
    • +
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+

Examples

+
fix 1 all mscg 1
+fix 1 all mscg 1 range name A B
+fix 1 all mscg 1 max 4 8 20
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+

Description

+

This fix applies the Multi-Scale Coarse-Graining (MSCG) method to +snapshots from a dump file to generate potentials for coarse-grained +simulations from all-atom simulations, using a force-matching +technique (Izvekov, Noid).

+

It makes use of the MS-CG library, written and maintained by Greg +Voth’s group at the University of Chicago, which is freely available +on their MS-CG GitHub site. See instructions +on obtaining and installing the MS-CG library in the src/MSCG/README +file, which must be done before you build LAMMPS with this fix command +and use the command in a LAMMPS input script.

+

An example script using this fix is provided the examples/mscg +directory.

+

The general workflow for using LAMMPS in conjunction with the MS-CG +library to create a coarse-grained model and run coarse-grained +simulations is as follows:

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    +
  1. Perform all-atom simulations on the system to be coarse grained.
    2. +
  2. Generate a trajectory mapped to the coarse-grained model.
    3. +
  3. Create input files for the MS-CG library.
    4. +
  4. Run the range finder functionality of the MS-CG library.
    5. +
  5. Run the force matching functionality of the MS-CG library.
    6. +
  6. Check the results of the force matching.
    7. +
  7. Run coarse-grained simulations using the new coarse-grained potentials.
    8. +
+

This fix can perform the range finding and force matching steps 4 and +5 of the above workflow when used in conjunction with the +rerun command. It does not perform steps 1-3 and 6-7.

+

Step 2 can be performed using a Python script (what is the name?) +provided with the MS-CG library which defines the coarse-grained model +and converts a standard LAMMPS dump file for an all-atom simulation +(step 1) into a LAMMPS dump file which has the positions of and forces +on the coarse-grained beads.

+

In step 3, an input file named “control.in” is needed by the MS-CG +library which sets parameters for the range finding and force matching +functionalities. See the examples/mscg/control.in file as an example. +And see the documentation provided with the MS-CG library for more +info on this file.

+

When this fix is used to perform steps 4 and 5, the MS-CG library also +produces additional output files. The range finder functionality +(step 4) outputs files defining pair and bonded interaction ranges. +The force matching functionality (step 5) outputs tabulated force +files for every interaction in the system. Other diagnostic files can +also be output depending on the paramters in the MS-CG library input +script. Again, see the documentation provided with the MS-CG library +for more info.

+
+

The range keyword specifies which MS-CG library functionality should +be invoked. If on, the step 4 range finder functionality is invoked. +off, the step 5 force matching functionality is invoked.

+

If the name keyword is used, string names are defined to associate +with the integer atom types in LAMMPS. Ntype names must be +provided, one for each atom type (1-Ntype).

+

The max keyword specifies the maximum number of bonds, angles, and +dihedrals a bead can have in the coarse-grained model.

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+

Restrictions

+

This fix is part of the MSCG package. It is only enabled if LAMMPS was +built with that package. See the Making LAMMPS section for more info.

+

The MS-CG library uses C++11, which may not be supported by older +compilers. The MS-CG library also has some additional numeric library +dependencies, which are describd in its documentation.

+

Currently, the MS-CG library is not setup to run in parallel with MPI, +so this fix can only be used in a serial LAMMPS build and run +on a single processor.

+

Related commands: none

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+

Default

+

The default keyword settings are range off, max 4 12 36.

+
+

(Izvekov) Izvekov, Voth, J Chem Phys 123, 134105 (2005).

+

(Noid) Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J +Chem Phys 128, 134105 (2008).

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