142 lines
4.9 KiB
ReStructuredText
142 lines
4.9 KiB
ReStructuredText
.. index:: fix mscg
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fix mscg command
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================
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Syntax
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""""""
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.. parsed-literal::
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fix ID group-ID mscg N keyword args ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mscg = style name of this fix command
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* N = envoke this fix every this many timesteps
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* zero or more keyword/value pairs may be appended
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* keyword = *range* or *name* or *max*
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.. parsed-literal::
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*range* arg = *on* or *off*
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*on* = range finding functionality is performed
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*off* = force matching functionality is performed
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*name* args = name1 ... nameN
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name1,...,nameN = string names for each atom type (1-Ntype)
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*max* args = maxb maxa maxd
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maxb,maxa,maxd = maximum bonds/angles/dihedrals per atom
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Examples
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""""""""
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.. code-block:: LAMMPS
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fix 1 all mscg 1
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fix 1 all mscg 1 range name A B
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fix 1 all mscg 1 max 4 8 20
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Description
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"""""""""""
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This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
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snapshots from a dump file to generate potentials for coarse-grained
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simulations from all-atom simulations, using a force-matching technique
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(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
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It makes use of the MS-CG library, written and maintained by Greg Voth's
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group at the University of Chicago, which is freely available on their
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`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
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See instructions on obtaining and installing the MS-CG library in the
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src/MSCG/README file, which must be done before you build LAMMPS with
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this fix command and use the command in a LAMMPS input script.
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An example script using this fix is provided the examples/mscg
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directory.
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The general workflow for using LAMMPS in conjunction with the MS-CG
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library to create a coarse-grained model and run coarse-grained
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simulations is as follows:
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1. Perform all-atom simulations on the system to be coarse grained.
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2. Generate a trajectory mapped to the coarse-grained model.
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3. Create input files for the MS-CG library.
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4. Run the range finder functionality of the MS-CG library.
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5. Run the force matching functionality of the MS-CG library.
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6. Check the results of the force matching.
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7. Run coarse-grained simulations using the new coarse-grained potentials.
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This fix can perform the range finding and force matching steps 4 and 5
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of the above workflow when used in conjunction with the :doc:`rerun
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<rerun>` command. It does not perform steps 1-3 and 6-7.
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Step 2 can be performed using a Python script (cgmap), which defines the
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coarse-grained model and converts a standard LAMMPS dump file for an
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all-atom simulation (step 1) into a LAMMPS dump file which has the
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positions of and forces on the coarse-grained beads. To use cgmap the
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following repositories need to be downloaded and installed.
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#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
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#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
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In step 3, an input file named "control.in" is needed by the MS-CG
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library which sets parameters for the range finding and force matching
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functionalities. See the examples/mscg/control.in file as an example.
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And see the documentation provided with the MS-CG library for more
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info on this file.
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When this fix is used to perform steps 4 and 5, the MS-CG library also
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produces additional output files. The range finder functionality
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(step 4) outputs files defining pair and bonded interaction ranges. The
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force matching functionality (step 5) outputs tabulated force files for
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every interaction in the system. Other diagnostic files can also be
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output depending on the parameters in the MS-CG library input script.
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Again, see the documentation provided with the MS-CG library for more
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info.
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----------
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The *range* keyword specifies which MS-CG library functionality should
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be invoked. If *on*, the step 4 range finder functionality is invoked.
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*off*, the step 5 force matching functionality is invoked.
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If the *name* keyword is used, string names are defined to associate
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with the integer atom types in LAMMPS. *Ntype* names must be provided,
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one for each atom type (1-Ntype).
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The *max* keyword specifies the maximum number of bonds, angles, and
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dihedrals a bead can have in the coarse-grained model.
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Restrictions
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""""""""""""
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This fix is part of the MSCG package. It is only enabled if LAMMPS was
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built with that package. Building the MSCG package also requires
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external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
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pages for more info.
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Currently, the MS-CG library is not set up to run in parallel with MPI,
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so this fix can only be used in a serial LAMMPS build and run on a
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single processor.
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Related commands
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""""""""""""""""
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none
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Default
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"""""""
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The default keyword settings are range off, max 4 12 36.
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----------
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.. _Izvekov:
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**(Izvekov)** Izvekov, Voth, J Chem Phys 123, 134105 (2005).
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.. _Noid:
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**(Noid)** Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J
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Chem Phys 128, 134105 (2008).
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