Drawing A Molecule for MD Simulations

When studying a molecular system, for example polymers in solution, the very first step is to prepare the molecule of interest. Here using the poly(ethylene oxide) or PEO as an example, the software Avogadro is used for the demonstration.

Though in this simple example, the PEO with 4 repeat units in the form of CH3-O-[CH2-CH2-O]N-CH3 (N=4 for this example) is demonstrated, the basic procedure is nearly the same for more complicated molecules. There are two ways to draw the molecule:

  • draw the molecule atom by atom manually
  • direct draw the molecule using the SMILES notations

The first method gives more design freedom of the molecule, which is very helpful in generating a molecular system, such as PEO-grafted gold nanopores (will emerge in a later tutorial). The latter, on the other hand, provides a fast way to finish the task.

Manually Draw the Molecule

(a) Go into the draw mode.

(b) Select atom type and draw the molecule.

(c) Use carbon atom for all backbone atom first, then correct it later.

(d) Do energy minimization (the E button) of the generated molecule to have a reasonable structure.

(e) Save the file in the pdb format which will be used for MD simulations.

Directly Draw the Molecule Using SMILES

One can also use the SMILES for convenient generation by the following steps:

  1. go to Build
  2. select Insert
  3. choose SMILES
  4. type COCCOCCOCCOCCOC
  5. done

What’s the next

With the generated PEO4.pdb file, the next step is running MD simulations with other followup work to do. Stay tuned!