Interactive simulation

DockerMakefiles/DockerMake.yml

@@ -10,7 +10,7 @@ _SOURCES_:
   - PySCF.yml
   - PythonTools.yml
   - SymMol.yml
-
+  - LAMMPS.yml
 
 _ALL_:
   - ambertools
@@ -24,7 +24,7 @@ _ALL_:
   - moldesign_complete
   - moldesign_notebook
   - moldesign_minimal
-
+  - lammps
 
 ##################################################
 # Base image definitions

DockerMakefiles/LAMMPS.yml

@@ -0,0 +1,52 @@
+lammps_requirements:
+  description: Base libraries for BOTH running and building LAMMPS
+  build: |
+    RUN apt-get -y update
+    RUN apt-get -y install \
+        bc \
+        ssh \
+        mpich2 \
+        python-dev \
+        libz-dev \
+        fftw3-dev
+
+    ENV PATH=${PATH}:/usr/lib
+    ENV PYTHONPATH=${PYTHONPATH}:/opt/lammps/python
+    ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/opt/lammps/src
+
+lammps_build:
+ requires:
+  - buildbase
+  - lammps_requirements
+ description: Build image for LAMMPS. Based on https://github.com/malramsay64/lammps-docker/blob/master/Dockerfile
+ build: |
+
+    RUN git clone https://github.com/lammps/lammps.git /opt/lammps && \
+        cd /opt/lammps && \
+        git fetch && \
+        git checkout stable
+
+    RUN cd /opt/lammps/src && \
+        make yes-ASPHERE yes-BODY yes-CLASS2 yes-COLLOID yes-COMPRESS yes-CORESHELL yes-DIPOLE yes-GRANULAR yes-KSPACE yes-MANYBODY && \
+        make yes-MC yes-MOLECULE yes-OPT yes-PERI yes-PERI yes-PYTHON yes-REPLICA yes-RIGID yes-SHOCK yes-SNAP yes-SRD
+
+    # RUN cd /opt/lammps/src && \
+    #     make serial mode=shlib -j4
+
+    RUN cd /opt/lammps/src && \
+        make mpi mode=shlib -j4 MPI_INC="-DMPICH_SKIP_MPICXX -I/usr/include/mpich" MPI_LIB="-Wl,-rpath,/usr/lib/mpich/lib -L/usr/lib/mpich/lib -lmpl -lmpich"
+
+    RUN cd /opt/lammps/python && \
+        python install.py
+
+lammps:
+  description: Deployable LAMMPS image
+  build_directory: buildfiles/lammps/
+  requires:
+    - python_deploy_base
+    - lammps_requirements
+  copy_from:
+    lammps_build:
+      /usr/local/lib/python2.7/dist-packages: /usr/local/lib/python2.7/
+      /usr/lib: /usr
+      /opt/lammps: /opt

moldesign/_notebooks/Example 6. LAMMPS energy model and integrator.ipynb

@@ -0,0 +1,150 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import moldesign as mdt\n",
+    "from moldesign import units as u\n",
+    "import ipywidgets as ipy"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from moldesign.models.lammps_model import LAMMPSPotential\n",
+    "import parmed as med\n",
+    "# mdt.configure()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mol = mdt.from_pdb('1yu8')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mol = mdt.Molecule(mol.residues[0:10])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mdmol = mdt.assign_forcefield(mol)\n",
+    "atom = mdmol.atoms[13]\n",
+    "print \"Done parameterizing\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print mdmol.write('pdb')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "######### Create LAMMPSInteractive model and run NVT simulation #########\n",
+    "mdmol.set_energy_model(mdt.models.LAMMPSInteractive)\n",
+    "\n",
+    "data = mdmol.energy_model.get_lammps_data()\n",
+    "print"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mdmol.calculate()\n",
+    "mdmol.set_integrator(integrator=mdt.integrators.LAMMPSLangevin, timestep=1.0*u.fs,\n",
+    "                     temperature=300.0*u.kelvin, frame_interval=50.0*u.fs, constrain_hbonds=False, constrain_water=False)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "mdmol.energy_model.apply_force(mdmol.atoms[11:20], [10.0, 0.0, 3.0] * u.kcalpermol/u.angstrom)\n",
+    "mytraj = mdmol.run(200 * u.fs)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 2",
+   "language": "python",
+   "name": "python2"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}

moldesign/_tests/test_mm.py

@@ -122,3 +122,54 @@ def test_minimization_reduces_energy(objkey, request):
     mol = request.getfuncargvalue(objkey)
     traj = mol.minimize()
     assert mol.calculate_potential_energy() < e1
+
+@typedfixture('hasmodel')
+def protein_stripped_amber_forcefield_lammps():
+    mol = mdt.from_pdb('1yu8')
+    mol = mdt.Molecule([res for res in mol.residues if res.type == "protein"])
+    newmol = mdt.assign_forcefield(mol)
+
+    # Set Potential energy model
+    newmol.set_energy_model(mdt.models.LAMMPSPotential)
+    newmol.calculate()
+
+    # Set Interactive energy model
+    newmol.set_energy_model(mdt.models.LAMMPSInteractive)
+    newmol.calculate()
+    newmol.energy_model.apply_force(atoms=newmol.atoms[11:20], vector=[10.0, 10.0, 0.0] * u.kcalpermol / u.angstrom)
+    newmol.energy_model.reset_force()
+    return newmol
+
+@typedfixture('hasmodel')
+def protein_amber_forcefield_lammps():
+    mol = mdt.from_pdb('1yu8')
+    newmol = mdt.assign_forcefield(mol)
+
+    # Set Potential energy model
+    newmol.set_energy_model(mdt.models.LAMMPSPotential)
+    newmol.calculate()
+
+    # Set Interactive energy model
+    newmol.set_energy_model(mdt.models.LAMMPSInteractive)
+    newmol.calculate()
+    newmol.energy_model.apply_force(atoms=newmol.atoms[11:20], vector=[10.0, 10.0, 0.0] * u.kcalpermol / u.angstrom)
+    newmol.energy_model.reset_force()
+    return newmol
+
+def test_lammps_shake_constrain_hbonds(protein_stripped_amber_forcefield_lammps):
+    mdmol = protein_stripped_amber_forcefield_lammps
+    mol = mdt.from_pdb('1yu8')
+    newmol = mdt.assign_forcefield(mol)
+    newmol.set_energy_model(mdt.models.LAMMPSPotential)
+
+    # Test without constraints
+    mdmol.set_integrator(mdt.integrators.LAMMPSLangevin, timestep=2.0*u.fs, temperature=300*u.kelvin, frame_interval=10.0*u.fs, constrain_hbonds=False, constrain_water=False)
+    traj = mdmol.run(1000*u.fs)
+
+    assert len(traj) > 0
+
+    # Test with constraints. Should raise NotImplementedError
+    mdmol.set_integrator(mdt.integrators.LAMMPSLangevin, timestep=2.0*u.fs, temperature=300*u.kelvin, frame_interval=10.0*u.fs, constrain_hbonds=True, constrain_water=True)
+    with pytest.raises(NotImplementedError):
+	traj = mdmol.run(1000*u.fs);
+

moldesign/integrators/__init__.py

@@ -1,3 +1,4 @@
 from . import base
 from .verlet import *
 from .openmm import *
+from .lammps_integrator import *