InSilicoLab for Chemistry

InSilicoLab for Chemistry offers a complete workspace for a Chemist who wishes to perform Quantum Chemistry calculations. The portal assists in preparing input for different QC applications, categorizes the input data, and facilitates the result analysis. The portal is available at https://insilicolab.grid.cyfronet.pl/.

Features

Data categorisation - all the input data - molecules or larger structures - are described with metadata to enable searching and categorisation. The information about each structure contains:

  • Molecular Formula
  • Smiles - an ASCII representation of a molecule; see also http://www.daylight.com/smiles/
  • Annotations - descriptions or comments added to a structure.
  • Tags - short keywords describing the structure.

 

JMol viewer - enabling preview of all the molecule structures right from the browser.

 

Trajectory Sculptor - an advanced tool for manipulation of Molecular Dynamics trajectories. It enables reducing the input system by:

  • Extracting only the relevant parts of the input structure (based on one frame of the trajectory). The molecules to be extracted are defined by the user, who specifies what kind of molecules are of interest, and what requirements they have to meet.
  • Choosing only a number of frames from the whole trajectory.

 

Application-specific forms - depending on the chosen Quantum Chemistry application a specific form is provided for input parameters.

 

Conformation scan form - enables generating multiple similar molecules that are a result of transformation of the initial molecule by rotation at a given bond, angle or dihedral.

 

Automatic parallelisation - in case the input data requires performing several computations, they are automatically configured and sent to a computing infrastructure. This will happen in two situations:

  • Multiple input geometries are specified manually,
  • Conformation scan is configured for an input molecule.

 

Automatic results analysis - the computation results are automatically parsed to extract relevant information (if available):

  • Atom coordinates of all the resulting structures
  • Molecular electronic energies after SCF
  • Molecular electronic energies with Möller-Plesset corrections
  • Molecular energies with Coupled Cluster corrections
  • Spin squared value
  • Net charge of the system
  • Multiplicity of the system

The original application output files are also available for download.

 

Advanced computation options - optimization of the computation parameters on the e-Infrastructure - read more...

Quantum Chemistry Applications

The portal offers access to three Chemistry applications:

Documentation

Screenshots

The effect of trajectory frame transformation done with the Trajectory Sculptor.

The effect of trajectory frame transformation done with the Trajectory Sculptor

 

Results of a molecule optimization performed with GAMESS.

Results of a molecule optimization performed with GAMESS

Demonstration

Using Trajectory Sculptor to prepare input for QC computation, and running the computation with this input.