2020 Update

This proejct is very dead. It has been superseded by better tools. For example, see our latest work

Summary

Force-matching and utilities package. Supports input from Gromacs and Lammps. Not tested for input NAMD simulations. Outputs Lammps tabular potentials, input files, and plain text tabular potentials. Can be used independently for topology reduction in coarse-graining.

License

MIT

Example 1: Coarse-graining a Trajectory of Water

The ForcePy module can be used to coarse-grained a trajectory. In this example, we'll convert an all-atom water simulation to a 2-site water model.

The first step is to import the necessary libraries:

from MDAnalysis import Universe
from ForcePy import *

Next, we load the fine-grained trajectory. The first file is the structure (pdb, tpr, gro, or psf) and the second file is the trajectory. Note that the tpr file reader depends highly on what version of gromacs with which the tpr file was created. See the help page about the tpr file format support in MDAnalysis. The code to load the fine-grained trajectory is:

fine_uni = Universe("foo.tpr", "foo.trr")
fine_uni.trajectory.periodic = True #NOTE: You MUST set this flag yourself

Now we create a coarse-grained trajectory using the fine-grained trajectory as an input:

coarse_uni =CGUniverse(fine_uni, selections=['name OW', 'name HW1 or name HW2'], 
                      names=['O', 'H2'], 
                       collapse_hydrogens=False)

The selections variable is an array of strings. Each string is a Charmm atom selection string. Note, these are very similar to VMD selection string. You may test them out using the following snippet::

selected_atoms = fine_uni.selectAtoms('name OW')
for a in selected_atoms:
    print a

In the example above water oxygen is the first string and water hydrogens are the second string. The next variable, names, is optional and is the array of names to be given to the selections. It is an array of strings the same length as selections. If names is not given, then the atoms in the resulting coarse-grained trajectory will have numbers as their names. The last variable, collapse_hydrogens, can be True or False. If it's True, then all hydrogens will automatically be included in neighboring atoms which are selected. So, for example, if you select a carbon, all its hydrogens will be included. Its default is False.

Now that you have a coarse-grained trajectory, you may write out the structure or trajectory using the following syntax:

write_structure(coarse_uni, "cg_foo.pdb")
write_structure(coarse_uni, "cg_foo.pdb", bonds='all')
write_trajectory(coarse_uni, "cg_foo.dcd")

The coarse-grained trajectory is also a valid MDAnalysis object and you may perform any analysis techniques on it from the MDAnalysis package.

Adding Bonds

Bonding information isn't always included in pdb files. To add a bond manually, use this line of code:

add_residue_bonds(coarse_uni, 'name O', 'name H2')    

This will bond all atoms named O with all atoms named H2 within each residue. To add bonds between residues, use this line of code:

add_sequential_bonds(coarse_uni, 'name C', 'name N')    

The two selection strings will be the bonded parts of each residue.

Example 2: Coarse-graining a Protein

Here are some examples of coarse-graining a protein with increasingly more coarse models

3-Beads per Residue

from MDAnalysis import Universe
from ForcePy import *

protein_file = 'foo.pdb'
fine_uni = Universe(protein_file)

cgu_1 = CGUniverse(fine_uni, ['name O or C', 'name N or name CA', '((not name C) and (not name O)) and ((not name n) and (not name CA))'], ['O', 'CA', 'S'], collapse_hydrogens=True)

add_residue_bonds(cgu_1, 'name O', 'name CA')
add_residue_bonds(cgu_1, 'name CA', 'name S')
add_sequential_bonds(cgu_1, 'name CA', 'name CA')
write_structure(cgu_1, 'cg_1.pdb', bonds='all')

The first bead is the carbonyl group, the second is the C-alpha and nitrogen, and the final is the side-chain.

1-Bead per Residue

cgu_2 = CGUniverse(fine_uni, ['all'])
add_sequential_bonds(cgu_2)
write_structure(cgu_2, 'cgu_2.pdb', bonds='all')

This is much simpler. The names are omitted for the beads and it is not necessary to pass selection strings to add_sequential_bonds() since there is only one atom in each residue.

3-Residues per Bead

Finally, here is how to put multiple residues into single beads. An array must be passed to the CGUniverse constructor which has a length of the desired number of beads and the array contains arrays of indices corresponding to the fine-grain residue indices. For example, to put residues 1,2,3 into a bead and residues 4,5 into another bead this array will accomplish that: [[1,2,3], [4,5]]. Here is a complete example of reducing every three residues into one bead:

protein_length = len(fine_uni.residues)
reduction_map = [[3 * x, 3 * x + 1, 3 * x + 2] for x in range(protein_length / 3)]
cgu_3 = CGUniverse(fine_uni, ['all'],
                   residue_reduction_map=reduction_map)
add_sequential_bonds(cgu_3)
write_structure(cgu_3, 'cgu_3.pdb', bonds='all')

Force-Matching

Let's use again the example of 2-site water. If the original all-atom trajectory had forces, then we may use this file for force-matching.

from MDAnalysis import Universe
from ForcePy import *
import pickle
    
fgu = Universe('topol.tpr', 'traj.trr')
fgu.trajectory.periodic = True #NOTE: You MUST set this flag yourself, since there is no indication in the TPR files
cgu = CGUniverse(fgu, ['name OW', 'name HW1 or name HW2'], ['O', 'H2'], False)
add_residue_bonds(cgu, 'name O', 'name H2')
fm = ForceMatch(cgu) 

At this point, we have a ForeMatch object which contains the coarse-grained universe. Now we need to set-up the force field which will be force-matched to fit the coarse-grained trajectory forces (which themselves came from the all-atom trajectory).

ff = FileForce() #This just says the forces are found in the universe passed to the ForceMatch object
#Set this force as the reference force to be matched
fm.add_ref_force(ff)    

pair_mesh = Mesh.UniformMesh(0,12,0.05) #This is the mesh on which the force-field will be built. It is in Angstroms
pairwise_force = SpectralForce(Pairwise, pair_mesh, Basis.UnitStep)  
#Copy this force type and clone it for each pair-interaction type
fm.add_and_type_pair(pairwise_force)
#This is a harmonic bond that will be fixed to the energy minimum of the bonds with a harmonic constant of 500 kJ/mol
bond_force = FixedHarmonicForce(Bond, 500, cutoff=1) 
fm.add_and_type_pair(bond_force)

At this point, can now force match. To do it in serial:

fm.force_match()

You may also pass an iterations argument to use less than the entire trajectory. To do it in parallel (note you must have started using mpirun, mpiexec, or aprun depending on your MPI environment)

fm.force_match_mpi()

One thing about MPI runs is that it's much faster to pre-compute all the trajectory mapping at the beginning so that it isn't repeated on each node. This may be done by changing a line:

cgu = CGUniverse(fgu, ['name OW', 'name HW1 or name HW2'], ['O', 'H2'], False)
#this will precompute the cg trajectory at every frame; this may take some time
cgu = cgu.cache()

Finally, to write out the a set of lammps scripts to use the new force field, run

fm.write_lammps_scripts()

Installing ForcePy

Dependencies

• Python2.7
• scipy/numpy
• MDAnalysis (development branch)

Optional Dependencies

• MPI4Py (for parallel force-matching)
• matplotlib (for plotting)

Install

First install the development branch of MDAnalysis

git clone https://code.google.com/p/mdanalysis/ mdanalysis
cd mdanalysis
git checkout develop
cd package
python setup.py install --user

Next install ForcePy

cd ../../
git clone https://github.com/whitead/ForcePy.git ForcePy
cd ForcePy
python setup.py install --user

If you see a long list of errors, check the first few. If it says it can't find arrayobject.h, then your numpy headers are not being found. If you're in the Voth group and using the Enthought python distribution, try adding this line to your ~/.profile or ~/.bash_profile file:

export C_INCLUDE_PATH=/opt/local/include:/Library/Frameworks/EPD64.framework/Versions/7.2/lib/python2.7/site-packages/numpy/core/include:$C_INCLUDE_PATH

Architecture Notes

The main class to utilize is a ForceMatch class. This class takes in one or more reference Force objects that define the forces to match. For example, a FileForce will read in forces from a file. The ForceMatch class also takes one or more target Force objects, which are the functional forms that are going to match the reference forces. Some Force objects contain a static class variable that points to a ForceCategory that contains useful methods/variables. For example, the Pairwise contains a neighborlist implementation.

Regularizers may be added to force objects as well by calling the add_regularizer method.

The SpectralForce is a linear combination of basis functions. This is usually a good choice. The SpectralForce requires a mesh and basis function. Currently only UniformMesh is implemented. For the basis functions, UnitStep, Quartic, and Gaussian are implemented.

A given Force may be 'specialized' to work on only a certain type or type pair. This may be done by calling specialize_type before it is added to a ForceMatch class.

In order to simplify constructing potentials for many type pairs, there are utility functions on the ForceMatch class to construct all possible pairs. add_and_type_pairs copies a force as many times as needed to have a unique force for every possible pair-pair interaction.

Meshes

• Uniform mesh

Basis functions

• UnitStep
• Quartic
• Gaussian

Forces

• FileForce
• LammpsFileForce
• SpectralPairwiseForce
• AnalyticForce
• LJForce
• FixedHarmonicForce

Regularizers

• SmoothRegularizer
• L2Regularizer