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Small Molecule Molecular Dynamics Simulation


Lipids, monosaccharides, second messengers, other natural products and metabolites, pharmaceuticals, and other foreign compounds are examples of small molecules, which are low molecular weight molecules. Compared to huge molecules like proteins, they are distinct. Small molecules are major functional players in biology and play important roles in practically every element of life. In the study of tiny molecules, molecular dynamics (MD) simulation is one of the most important techniques.

Alfa Chemistry offers its customers world-class small molecule MD simulation services. For applications in drug discovery, MD simulation has been widely used. Applications being researched include lipid membrane permeability, protein-ligand binding, protein-protein interactions, and partition coefficients. The benefits of MD simulations are the ability to calculate atomic details and thermodynamic properties, such as free energy of binding.

Small Molecule Molecular Dynamics Simulation

Our Services

Alfa Chemistry explores small analytical structures and interactions using molecular dynamics (MD) modeling techniques, among other things. We concentrate in particular on research examining how model membranes are affected by water, small molecule drugs and molecules that resemble drugs, short peptides, and cryoprotectants.

Project NameSmall Molecule Molecular Dynamics Simulation Service
DeliverablesWe provide all raw data and analysis services to our customers.
Samples RequirementThe initial structure of the small molecule, PDB ID, etc.
Timeline DecideAccording to customers' needs
PricePlease contact us for an inquiry

GROMACS offers a wide range of capabilities in molecular dynamics simulation, which we usually use to simulate organic small molecules. We need to generate the topology for the molecule and then the generated file will be used for the simulation. The steps for simulating organic small molecules using GROMACS are as follows.

  • Obtain the molecular structure: We will use different software (e.g. Marvin Sketch) to draw the molecule, which can also be downloaded from Pubchem (if available). We need the structure in mol2 format to generate the topology. If a PDB file is available, then we can use Pymol for file conversion.
  • Preparing the molecule: If I downloaded the molecule in SDF format from Pubchem, we will use Avogadro to convert it to mol2 format.
  • Generate molecular topology: Depending on the force field chosen by the customer, there are different programs available for generating the topology of the molecule.
  • Defining the box: Now, we need to define a box around the molecule.
  • Dissolve the molecule: You may wish to dissolve your molecule in a solvent mixture. We will follow specific steps for solubilization using a solvent mixture. The added solvent molecules will be reflected in the topology file (
  • Energy Minimization: Now, run energy minimization using mdrun.
  • Running the MD simulation: We will run the MD simulation for 30 ns or 50/60 ns. 30 ns should be sufficient, but if the RMSD is not a straight line, increase the duration of the MD run.


Our Advantages

  • The researchers all come from renowned universities or research centers and have extensive backgrounds in the simulation of protein molecular dynamics.
  • On a wide range of linked themes, we have either worked on our own or offered support to our clients. Numerous findings from the calculations and tests have been published in a number of major SCI publications in the field of life sciences.

Alfa Chemistry is committed to providing customers with high-end and high-quality technical services, and has rich practical experience and core technologies in small molecule MD simulation. This service has proven to be very helpful at all stages of drug development by providing accurate simulations of the structural behavior of small molecules. Please contact us.

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