# Available Science Applications¶

The following codes have been optimized to run on Cascade and the consulting
staff have written submission scripts (located in
`/home/scicons/cascade/bin/`

) for most applications to facilitate setting
up Cascade jobs for these codes.

Running jobs are subject to the limits set within our Computational Jobs Policy.

## Biology and Bioinformatics¶

### Biocellion¶

Biocellion simulates biological systems with a large number of cells, capturing individual cell behaviors, interactions between cells, and interactions of cells with their biotic and abiotic environment.

### Diamond¶

Diamond can be used for high-throughput DNA or protein sequence alignment and database searches analogous to BLAST.

### EMAN¶

EMAN is an image processing suite with a primary focus on processing data from transmission electron microscopes. It performs single particle reconstructions, single particle cryo-ET, 2-D crystallography and whole-cell tomography.

### HMMer / MaxRebo¶

MaxRebo is tool developed at PNNL to perform high-throughput HMMer searches against hidden Markov model libraries of protein families. The available HMM libraries are: Pfam, TIGRFAM, dbCAN, FOAM, and PhyloFacts. The input sequence data can be protein or DNA sequences (DNA sequences will be translated).

### RELION¶

RELION employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy (cryo-EM).

### Scalablast¶

ScalaBLAST is an `mpi`

implementation of NCBI BLAST that can be used for
protein sequence alignment and database searching.

```
submit_scalablast
```

## Environmental and Hydrological¶

## Classical Molecular Dynamics¶

### Amber¶

Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

```
submit_amber
```

### CPMD¶

CPMD is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics.

### GROMACS¶

GROMACS performs molecular dynamics simulations, and is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions.

### LAMMPS¶

LAMMPS can be used to model solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems.

```
submit_lammps
```

## Quantum Chemistry¶

### ADF¶

ADF is a quantum chemistry software package based on Density Functional Theory (DFT). It consists of the molecular DFT code ADF, the periodic DFT code BAND, and the post-ADF COSMO-RS program for liquid thermodynamics, as well as graphical interfaces for these engines and source code for ADF and BAND.

```
submit_adf
```

Important

Users need to provide their own license for ADF. Once we have proof of your ownership, we will make ADF available to you.

### CP2K¶

```
submit_cp2k
```

### GAMESS¶

GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation.

```
submit_gamess
```

### Molpro¶

Molpro is a complete system of ab initio programs for molecular electronic structure calculations. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods.

```
submit_molpro
submit_molpro_2012.1.8
```

### NWChem¶

NWChem is a scalable computational Chemistry software actively developed and maintained by the EMSL staff.

```
submit_nwchem
submit_nwchem6.1.1
submit_nwchem6.3
```

### Quantum ESPRESSO¶

Quantum ESPRESSO is a software suite for ab initio quantum chemistry methods of electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

### VASP¶

VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.

```
submit_vasp
submit_vasp4
submit_vasp4_so
submit_vasp5
submit_vasp5_so
submit_vasp5_ts
```

Important

Users need to provide their own license for VASP. Once we have proof of your ownership, we will make VASP available to you.