Conformers Generation with Multiple Molecules

../../_images/conformers_22_0.png

See also

Example illustrating how to generate conformers with AMS.

This example is only compatible with AMS2024.

To follow along, either

Note

Conformers generation depends on random numbers. You are likely to get somewhat different results if you run this example!

Lets see how two alanine molecules orient themselves using CREST conformer generation. To do this we will constrain the system in a spherical region using the SphericalWall constraint. We start by setting up a system of two alanine molecules in a relatively small space.

Initial imports

import scm.plams as plams
from scm.conformers import ConformersJob
from scm.conformers.plams.plot import plot_conformers
import numpy as np
import matplotlib.pyplot as plt
import os
plams.init()

PLAMS working folder: /path/plams_workdir.005

Single alanine molecule

smiles = 'CC(N)C(=O)O'
alanine = plams.from_smiles(smiles)
plams.plot_molecule(alanine)
../../_images/conformers_4_0.png

Initial system: alanine dimer

Pack two alanine molecules in a sphere with a density of 0.5 kg/L.

density = 0.5
mol = plams.packmol(alanine, n_molecules=2, density=density, sphere=True)

Translate the molecule to be centered around the origin (needed for SphericalWall later):

mol.translate(-np.array(mol.get_center_of_mass()))

plams.plot_molecule(mol, rotation='0x,0y,90z')
../../_images/conformers_10_0.png

Calculation setup

To determine the radius of the SphericalWall we measure the size of the initial dimer.

dists = plams.distance_array(mol, mol)
max_dist = np.max(dists)
diameter = 1.33 * max_dist
radius = diameter / 2
print(f'Largest distance between atoms: {max_dist:.3f} ang.')
print(f'Radius: {radius:.3f} ang.')

Largest distance between atoms: 9.882 ang.
Radius: 6.572 ang.

Now we can set up the Crest conformer generation job, with the appropriate spherical wall constraining the molecules close together.

settings = plams.Settings()
settings.input.ams.EngineAddons.WallPotential.Enabled = 'Yes'
settings.input.ams.EngineAddons.WallPotential.Radius = radius
settings.input.ams.Generator.Method = 'CREST'
settings.input.ams.Output.KeepWorkDir = 'Yes'
settings.input.ams.GeometryOptimization.MaxConvergenceTime = 'High'
settings.input.ams.Generator.CREST.NCycles = 3  # at most 3 CREST cycles for this demo
settings.input.GFNFF = plams.Settings()

Run the conformers job

Now we can run the conformer generation job.

job = ConformersJob(molecule=mol, settings=settings)
job.run()
#ConformersJob.load_external("plams_workdir/conformers/conformers.rkf")  # load from disk instead of running the job

[11.03|15:40:06] JOB conformers STARTED
[11.03|15:40:06] JOB conformers RUNNING
[11.03|15:48:41] JOB conformers FINISHED
[11.03|15:48:41] JOB conformers SUCCESSFUL

<scm.conformers.plams.interface.ConformersResults at 0x7f97c3b278e0>

rkf = job.results.rkfpath()
print(f"Conformers stored in {rkf}")

Conformers stored in /path/plams_workdir.005/conformers/conformers.rkf

This job will run for approximately 15 minutes.

Results

Here we plot the three lowest-energy conformers.

plot_conformers(job);
../../_images/conformers_22_0.png

You can also open the conformers in AMSmovie to browse all conformers 1000+ conformers:

!amsmovie {rkf}

Finish PLAMS

plams.finish()

[11.03|15:49:18] PLAMS run finished. Goodbye

Complete Python code

#!/usr/bin/env amspython
# coding: utf-8

# Lets see how two alanine molecules orient themselves using CREST conformer generation.
# To do this we will constrain the system in a spherical region using the `SphericalWall` constraint.
# We start by setting up a system of two alanine molecules in a relatively small space.

# ## Initial imports

import scm.plams as plams
from scm.conformers import ConformersJob
from scm.conformers.plams.plot import plot_conformers
import numpy as np
import matplotlib.pyplot as plt
import os

plams.init()


# ## Single alanine molecule

smiles = "CC(N)C(=O)O"
alanine = plams.from_smiles(smiles)
plams.plot_molecule(alanine)


# ## Initial system: alanine dimer

# Pack two alanine molecules in a sphere with a density of 0.5 kg/L.

density = 0.5
mol = plams.packmol(alanine, n_molecules=2, density=density, sphere=True)


# Translate the molecule to be centered around the origin (needed for SphericalWall later):

mol.translate(-np.array(mol.get_center_of_mass()))


plams.plot_molecule(mol, rotation="0x,0y,90z")


# ## Calculation setup

# To determine the radius of the `SphericalWall` we measure the size of the initial dimer.

dists = plams.distance_array(mol, mol)
max_dist = np.max(dists)
diameter = 1.33 * max_dist
radius = diameter / 2
print(f"Largest distance between atoms: {max_dist:.3f} ang.")
print(f"Radius: {radius:.3f} ang.")


# Now we can set up the Crest conformer generation job, with the appropriate spherical wall constraining the molecules close together.

settings = plams.Settings()
settings.input.ams.EngineAddons.WallPotential.Enabled = "Yes"
settings.input.ams.EngineAddons.WallPotential.Radius = radius
settings.input.ams.Generator.Method = "CREST"
settings.input.ams.Output.KeepWorkDir = "Yes"
settings.input.ams.GeometryOptimization.MaxConvergenceTime = "High"
settings.input.ams.Generator.CREST.NCycles = 3  # at most 3 CREST cycles for this demo
settings.input.GFNFF = plams.Settings()


# ## Run the conformers job

# Now we can run the conformer generation job.

job = ConformersJob(molecule=mol, settings=settings)
job.run()
# ConformersJob.load_external("plams_workdir/conformers/conformers.rkf")  # load from disk instead of running the job


rkf = job.results.rkfpath()
print(f"Conformers stored in {rkf}")


# This job will run for approximately 15 minutes.

# ## Results
# Here we plot the three lowest-energy conformers.

plot_conformers(job)


# You can also open the conformers in AMSmovie to browse all conformers 1000+ conformers:


# ## Finish PLAMS

plams.finish()