Package Programs List (Molecular Science)

Last update: Sep 10, 2025.

Compilers and Libraries

Most packages are installed under /apl.
Please check this page for Basic Biology software packages.

nameversionnote
GCC8.5.0*(system default package)
9.2.1module: gcc-toolset/9 (gcc-toolset-9)
10.3.1module: gcc-toolset/10 (gcc-toolset-10)
11.2.1module: gcc-toolset/11 (gcc-toolset-11)
12.2.1module: gcc-toolset/12 (gcc-toolset-12)
13.3.1module: gcc-toolset/13 (gcc-toolset-13)
14.2.1module: gcc-toolset/14 (gcc-toolset-14)
AOCC5.0.0module: aocc/5.0.0
4.2.0module: aocc/4.2.0
4.1.0module: aocc/4.1.0
4.0.0module: aocc/4.0.0
3.2.0module: aocc/3.2.0
AOCL5.0.0module: aocl/5.0.0-aocc5.0 (built with AOCC), aocl/5.0.0-gcc13.2 (built with GCC)
4.2.0module: aocl/4.2.0-aocc4.2 (built with AOCC), aocl/4.2.0-gcc13.1 (built with GCC)
4.1.0module: aocl/4.1.0-aocc4.1 (built with AOCC), aocl/4.1.0-gcc13.1 (built with GCC)
4.0module: aocl/4.0-aocc4.0 (built with AOCC), aocl/4.0-gcc11.2 (built with GCC)
3.2.0module: aocl/3.2.0-aocc3.2 (built with AOCC), aocl/3.2.0-gcc11.2 (built with GCC)
Python [1]3.6.8*(/usr/bin/python3)
2.7.18*(/usr/bin/python2)
3.11.11(/usr/bin/python3.11)
3.9.20(/usr/bin/python3.9)
3.12.9miniforge3 env (/apl/conda/20250310; source conda_init.sh or conda_init.csh to load env)
3.10.13 (base)
3.12.2 (gpuenv)
miniforge3 env (/apl/conda/20240305; source conda_init.sh or conda_init.csh to load env)
3.10.9miniforge3 env (/apl/conda/20230214; source conda_init.sh or conda_init.csh to load env)
NVIDIA HPC SDK25.7, 25.3
24.9, 24.3
23.9, 23.5
22.11
module: nvhpc/(version), nvhpc/(version)-byo, nvhpc/(version)-nompi
Intel oneAPI Compiler Runtime [2]2025.2.1, 2025.2.0, 2025.1.1, 2025.1.0, 2025.0.4, 2025.0, 2024.2.1, 2024.2, 2024.1.0, 2024.0.2, 2024.0, 2023.2.0, 2023.1.0, 2023.0.0, 2022.2.1, 2022.0.2module: compiler-rt/(version)
Intel MKL2025.2.0, 2025.1.0, 2025.0.0.1, 2025.0, 2024.2, 2024.1, 2024.0, 2023.2.0, 2023.1.0, 2023.0.0, 2022.2.1, 2022.0.2module: mkl/(version)

2025.0.0.1 =>
(major 2025, minor 0, update 0, patch 1; 2025.0.1 is the correct name?)
Intel MPI2021.16.1, 2021.16, 2021.15, 2021.14.1, 2021.14, 2021.13, 2021.12, 2021.11, 2021.10.0, 2021.9, 2021.8, 2021.7.1, 2021.5.1module: intelmpi/(version)
CUDA12.9 Update 1module: cuda/12.9u1
12.8 Update 1*module: cuda/12.8u1
12.6 Update 2module: cuda/12.6u2
12.4 Update 1module: cuda/12.4u1
12.2 Update 2module: cuda/12.2u2
12.1 Update 1module: cuda/12.1u1
12.0module: cuda/12.0
11.6module: cuda/11.6
11.2module: cuda/11.2
Open MPI5.0.8, 5.0.6, 5.0.5, 5.0.1
4.1.8, 4.1.6, 4.1.5
3.1.6
module: openmpi/(version) (modules for each compiler available)
HPC-X2.16 (Open MPI 4.1.5)module: openmpi/4.1.5-hpcx2.16 (modules for each compiler available)
2.13.1 (Open MPI 4.1.5)module: openmpi/4.1.5-hpcx (modules for each compiler available)
2.11 (Open MPI 4.1.4)module: openmpi/4.1.4-hpcx (modules for each compiler available)
MVAPICH4.0, 3.0, 2.3.7module: mvapich/(version) (modules for GCC and AOCC available)
Julia1.11.3, 1.10.0, 1.8.5
1.10.8 (LTS), 1.6.7 (LTS)
module: julia/(version)
Apptainer/Singularity1.3.6(singularity is an alias of apptainer)

*: default version
[1]: you can install packages to your home directory by using "pip3 install (package name) --user" command. Installing miniforge might be another good choice. However, the initialization of conda environment might take long time (only upon first time; this is due to the fundamental mechanism of lustre filesystem). If you need only a few packages, you should install them to your home directory via "pip3".
[2]: Compilers (such as ifort, ifx) are not installed in /apl. In case you need Intel compilers, please install Intel oneAPI Base Toolkit or HPC Toolkit into your directory.

Application Software

The list of installed software is shown below. (Blacked out package names indicate that they have not yet been installed but will be installed.) For the manual/documentations, please visit the official website. Packages are installed under /apl directory which are accessible from both of frontend and computation nodes. See this page for detailed information about installation.

Please cick links in "install date" column to see installation details.

namedescription
versioninstall datejob sample path & note
ABClusterSoftware for cluster structure optimization and conformation search
3.0○ (2023-Nov-28)/apl/abcluster/3.0/samples
ABINIT-MPA software for fast Fragment-Molecular-Orbital (FMO) calculations.
v2r8○ (2025-Jan-7)/apl/ABINIT-MP/v2r8/samples
v2r4○ (2023-Feb-21)/apl/ABINIT-MP/v2r4/samples
v1r22○ (2023-Feb-21)/apl/ABINIT-MP/v1r22/samples
ADF(*9) (not available) 

AlphaFold

(version3)
(version2)

AI program for predictions of protein structure.
3.0.0
(Jan 16, 2025)
△ (2025-Jan-16)

/apl/alphafold/samples/3.0.0-20250116

GPU is required for inference.
AlphaFold3 model parameters must be requested and downloaded by users themselves.

3.0.0
(Nov 26, 2024)
△ (2024-Nov-26)

/apl/alphafold/samples/3.0.0-20241126

(same notice as above)

2.3.2△ (2024-Feb-8)/apl/alphafold/samples/2.3.2
2.3.1△ (2023-Feb-6)/apl/alphafold/samples/2.3.1
2.2.0△ (2022-Mar-14)/apl/alphafold/samples/2.2.0
2.1.1△ (2021-Nov-8)/apl/alphafold/samples/2.1.1
2.1.0△ (X-X-X)-
2.0.0 (2021/8/19)△ (2021-Aug-23)-
2.0.0 (2021/7/20)△ (2021-Jul-26)/apl/alphafold/samples/2.0.0-20210720
AmberPackage of molecular simulation programs.
24-update3 +
AmberTools25
○ (2025-May-19)/apl/amber/24u3+at25/samples
24-update3○ (2025-Mar-6)

/apl/amber/24u3/samples

There is a note on "module" command.
Please check notes of installation details.
(AmberTools24-update8)

24-update1○ (2024-Jun-11)

/apl/amber/24u1/samples

(AmberTools24-update2)

22-update4○ (2023-Aug-25)

/apl/amber/22u4/samples

(Ambertools23-update4)

22-update1○ (2023-Jan-X)

/apl/amber/22u1/samples

(AmberTools22-update4)

20-update13○ (2023-Jan-X)

/apl/amber/20u13/samples

(built with configure)

AutoDockAutomated docking tools
4.2.6○ (2023-Nov-24)/apl/autodock/4.2.6/samples
AutoDock-GPUGPU-enabled version of AutoDock
1.5.3○ (2023-Nov-24)/apl/autodock-gpu/1.5.3/samples
AutoDock VinaImproved version of AutoDock
1.2.7○ (2025-Jul-7)/apl/autodock-vina/1.2.7/samples
1.2.5○ (2023-Nov-24)/apl/autodock-vina/1.2.5/samples
CENSOProgram for evaluating structure ensembles at DFT level. 
2.1.4○ (2025-Sep-10)

/apl/censo/2.1.4/samples

anmr from ENSO 2.0.2 was added manually.

2.1.3○ (2025-May-1)

/apl/censo/2.1.3/samples

anmr from ENSO 2.0.2 was added manually.

1.2.0○ (2024-May-22)

/apl/censo/1.2.0/samples

(precomipled binary)
anmr and nmrplot.py from ENSO 2.0.2
were added manually.

ColabFoldSoftware to predict protein 3D structure from sequence information
1.5.5○ (2023-Apr-6)/apl/colabfold/1.5.5/samples

CP2K

A quantum chemistry and solid state physics software package.

2024.3

○ (2024-Oct-24)

/apl/cp2k/2024.3/samples

2024.2

○ (2024-Aug-22)

/apl/cp2k/2024.2/samples
2023.1

○ (2023-Apr-6)

/apl/cp2k/2023.1/samples
9.1

○ (2023-Jan-X)

/apl/cp2k/9.1/samples
CRESTA program for the automated exploration of the low-energy molecular chemical space.
3.0.1○ (2024-May-21)/apl/crest/3.0.1/samples
CRYSTALGeneral-purpose programs for the study of crystalline solids.
23-1.0.1○ (2024-Jul-19)

/apl/crystal/23-1.0.1/samples

(*21)

17-1.0.2○ (2023-Jan-X)

/apl/crystal/17-1.0.2/samples

(*21)

DaltonQuantum chemistry software capable of calculating various molecular properties
2020.1○ (2024-Nov-8)/apl/dalton/2020.1/samples
DFTB+Fast and efficient versatile quantum mechanical simulation software package
23.1○ (2023-Jul-19)
MPI / OpenMP

/apl/dftb+/23.1/mpi/samples
/apl/dftb+/23.1/nompi/samples

MPI and OpenMP versions available

DIRAC(*22)Computes molecular properties using relativistic quantum chemical methods (named after P. A. M. Dirac).
23.0○ (2023-May-8)/apl/dirac/23.0/samples
19.0○ (2023-Jan-27)/apl/dirac/19.0/samples

GAMESS

General atomic and molecular electronic structure system.
2024-R2(Jul15)○ (2024-Oct-31)

/apl/gamess/2024R2/samples

(NBO 7.0.10 enabled)

2023-R2(Sep30)○ (2023-Dec-7)

/apl/gamess/2023R2/samples

(NBO 7.0.10 enabled)

2022-R2(Sep30)○ (2023-Jan-X)

/apl/gamess/2022R2/samples

(NBO 7.0.7 enabled)

2021-R1(Jun30)○ (2023-Jan-X)

/apl/gamess/2021R1/samples

(NBO 7.0.7 enabled)

GaussianAb initio molecular orbital calculations.
16.C.02○ (2022-Mar-14)

(g16sub is available)
/apl/gaussian/16c02/samples

(NBO 7.0.10 enabled)

16.C.01○ (2019-Aug-2)

(g16sub is available)
/apl/gaussian/16c01/samples

(NBO 7.0.10 enabled)

16.B.01○ (2018-Mar-12)(g16sub is available)
/apl/gaussian/16b01/samples
09.E.01○ (2015-Dec-24)(g09sub is available)
/apl/gaussian/09e01/samples
GENESISMolecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes.
2.1.4○ (2025-Jan-10)
CPU / GPU
/apl/genesis/2.1.4/samples
/apl/genesis/2.1.4-CUDA/samples
2.1.2○ (2024-Jan-16)
CPU / GPU
/apl/genesis/2.1.2/samples
/apl/genesis/2.1.2-CUDA/samples
2.0.3○  (2023-Jan-X)
CPU / GPU
/apl/genesis/2.0.3/samples
/apl/genesis/2.0.3-CUDA/samples
GROMACSFast, Free and Flexible MD
2025.2○ (2025-May-27)
CPU / GPU

/apl/gromacs/2025.2/samples
/apl/gromacs/2025.2-CUDA/samples

NNP enabled (libtorch 2.7.0)

2024.6○ (2025-Aug-25)
CPU / GPU
/apl/gromacs/2024.6/samples
/apl/gromacs/2024.6-CUDA/samples
2024.5○ (2025-Jan-27)
CPU / GPU
/apl/gromacs/2024.5/samples
/apl/gromacs/2024.5-CUDA/samples
2024.4○ (2024-Nov-5)
CPU / GPU
/apl/gromacs/2024.4/samples
/apl/gromacs/2024.4-CUDA/samples
2024.2○ (2024-May-16)
CPU / GPU
/apl/gromacs/2024.2/samples
/apl/gromacs/2024.2-CUDA/samples
2023.5○ (2024-May-7)
CPU / GPU
/apl/gromacs/2023.5/samples
/apl/gromacs/2023.5-CUDA/samples
2023.4○ (2024-Jan-26)
CPU / GPU
/apl/gromacs/2023.4/samples
/apl/gromacs/2023.4-CUDA/samples
2023.2○ (2023-Aug-9)
CPU / GPU
/apl/gromacs/2023.2/samples
/apl/gromacs/2023.2-CUDA/samples
2022.6○ (2023-Jul-12)
CPU / GPU
/apl/gromacs/2022.6/samples
/apl/gromacs/2022.6-CUDA/samples
2022.4○ (2023-Jan-X)
CPU / GPU
/apl/gromacs/2022.4/samples
/apl/gromacs/2022.4-CUDA/samples
2021.7○ (2023-Apr-14)
CPU / GPU
/apl/gromacs/2021.7/samples
/apl/gromacs/2021.7-CUDA/samples
2021.6○ (2023-Jan-X)
CPU / GPU
/apl/gromacs/2021.6/samples
/apl/gromacs/2021.6-CUDA/samples
2021.4○ (2023-Jan-X)
CPU / GPU
/apl/gromacs/2021.4/samples
/apl/gromacs/2021.4-CUDA/samples
GRRMAutomated Exploration of Reaction Pathways.
23〇 (2024-Jan-11)

/apl/GRRM/23/samples

Application is required for use.
(multinode parallel available)

17(*5)(2021-Jan-27)

/apl/GRRM/17/samples

(multinode parallel available)

14○ (2015-Jul-29)/apl/GRRM/14/samples
LAMMPSLarge-scale Atomic/Molecular Massively Parallel Simulator.
22Jul2025
Update 1
○ (2025-Sep-4)
CPU(GCC,Intel) / GPU
/apl/lammps/2025-Jul22-u1/samples
/apl/lammps/2025-Jul22-u1-intel/samples
/apl/lammps/2025-Jul22-u1-CUDA/samples
22Jul2025○ (2025-Aug-6)
CPU(GCC,Intel) / GPU
/apl/lammps/2025-Jul22/samples
/apl/lammps/2025-Jul22-intel/samples
/apl/lammps/2025-Jul22-CUDA/samples
29Aug2024 Update 4○ (2025-Jul-29)
CPU(GCC,Intel) / GPU
/apl/lammps/2024-Aug29-u4/samples
/apl/lammps/2024-Aug29-u4-intel/samples
/apl/lammps/2024-Aug29-u4-CUDA/samples
29Aug2024 Update 3○ (2025-Jul-15)
CPU(GCC,Intel) / GPU
/apl/lammps/2024-Aug29-u3/samples
/apl/lammps/2024-Aug29-u3-intel/samples
/apl/lammps/2024-Aug29-u3-CUDA/samples
29Aug2024 Update 2○ (2025-Apr-18)
CPU(GCC,Intel) / GPU
/apl/lammps/2024-Aug29-u2/samples
/apl/lammps/2024-Aug29-u2-intel/samples
/apl/lammps/2024-Aug29-u2-CUDA/samples
29Aug2024 Update 1○ (2025-Feb-21)
CPU(GCC,Intel) / GPU
/apl/lammps/2024-Aug29-u1/samples
/apl/lammps/2024-Aug29-u1-intel/samples
/apl/lammps/2024-Aug29-u1-CUDA/samples
29Aug2024○ (2024-Sep-6)
CPU(GCC,Intel) / GPU
/apl/lammps/2024-Aug29/samples
/apl/lammps/2024-Aug29-intel/samples
/apl/lammps/2024-Aug29-CUDA/samples
2Aug23○ (2023-Oct-16)
CPU(GCC,Intel) / GPU

/apl/lammps/2023-Aug2/samples
/apl/lammps/2023-Aug2-intel/samples
/apl/lammps/2023-Aug2-CUDA/samples

Intel MPI

23Jun22 Update 2○ (2023-Jan-X)
CPU / GPU

/apl/lammps/2022-Jun23/samples
/apl/lammps/2022-Jun23-CUDA/samples

(netcdf off)

○ (2023-Apr-18)
CPU / GPU

/apl/lammps/2022-Jun23-impi/samples
/apl/lammps/2022-Jun23-impi-CUDA/samples

Intel MPI

29Sep21 Update 3○ (2023-Apr-18)
CPU / GPU

/apl/lammps/2021-Sep29-impi/samples
/apl/lammps/2021-Sep29-impi-CUDA/samples

Intel MPI

29Sep21○ (2023-Jan-X)
CPU / GPU

/apl/lammps/2021-Sep29/samples
/apl/lammps/2021-Sep29-CUDA/samples

(netcdf off)

LigandMPNNSoftware for designing sequences that bind to small ligands
 △ (2024-Mar-27)

/apl/LigandMPNN/20240327/samples

latest code on Mar 27, 2024

Molpro

Complete system of ab initio programs.

2025.1.0

△ (2025-Mar-14)

/apl/molpro/2025.1.0/samples
2024.3.0△ (2024-Nov-15)/apl/molpro/2024.3.0/samples
2024.2.0△ (2024-Sep-9)/apl/molpro/2024.2.0/samples
2024.1.0△ (2024-Mar-11)/apl/molpro/2024.1.0/samples
2023.2.0△ (2023-Oct-11)/apl/molpro/2023.2.0/samples
2023.1.0△ (2023-Sep-19)/apl/molpro/2023.1.0/samples
2022.3.0△ (2023-Jan-X)

/apl/molpro/2022.3.0/samples

(HPC-X)

△ (2023-May-18)

/apl/molpro/2022.3.0-mva/samples

(MVAPICH)

2022.2.2△ (2023-Jan-X)/apl/molpro/2022.2.2/samples
2021.3.1△ (2023-May-10)/apl/molpro/2021.3.1/samples
2015.1-44△ (2023-Jan-X)/apl/molpro/2015.1.44/samples
NAMDScalable molecular dynamics program.
3.0.1○ (2024-Oct-31)
MPI / SMP / SMP+CUDA
/apl/namd/3.0.1-mpi/samples
/apl/namd/3.0.1-smp/samples
/apl/namd/3.0.1-smp-cuda/samples
3.0○ (2024-Jul-5)
MPI / SMP / SMP+CUDA
/apl/namd/3.0-mpi/samples
/apl/namd/3.0-smp/samples
/apl/namd/3.0-smp-cuda/samples
3.0b7○ (2024-May-23)
MPI / SMP / SMP+CUDA
/apl/namd/3.0b7-mpi/samples
/apl/namd/3.0b7-smp/samples
/apl/namd/3.0b7-smp-cuda/samples
3.0b6○ (2024-Mar-6)
MPI / SMP / SMP+CUDA
/apl/namd/3.0b6-mpi/samples
/apl/namd/3.0b6-smp/samples
/apl/namd/3.0b6-smp-cuda/samples
3.0b2○ (2023-Apr-10)

/apl/namd/3.0b2-CUDA/samples

(GPU version only)

2.14○ (2023-Jan-X)
CPU / GPU
/apl/namd/2.14/samples
/apl/namd/2.14-CUDA/samples
NBODiscovery tool for chemical insights from complex wavefunctions.
7.0.10△ (2023-Feb-14)-
7.0.7△ (2023-Jan-X)-
NTChem(*17)Comprehensive new software of ab initio quantum chemistry made in Riken-RCCS from scratch.
2013.13.0.0○ (2023-Apr-28)/apl/ntchem/2013.13.0.0/samples
NWChemComputational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems
7.2.3○ (2025-Feb-27)
CPU / GPU
/apl/nwchem/7.2.3/samples
/apl/nwchem/7.2.3-intel/samples
7.2.2○ (2024-Mar-5)
CPU / GPU
/apl/nwchem/7.2.2/samples
/apl/nwchem/7.2.2-CUDA/samples
7.0.2○ (2023-Mar-6)/apl/nwchem/7.0.2/samples
6.8○ (2023-Mar-6)

-

for ReactionPlus

OmegaFoldA Protein Structure Prediction Software
1.1.0○ (2024-Jun-12)/apl/omegafold/1.1.0/samples

OpenBabel

Chemical toolbox designed to speak the many languages of chemical data

3.1.1

○ (2025-Mar-10)

-
OpenMMA high-performance toolkit for molecular simulation.
8.2.0○ (2025-Mar-6)/apl/openmm/8.2.0/samples
8.1.0○ (2023-Dec-5)/apl/openmm/8.1.0/samples

OpenMolcas

Quantum chemistry software. (Open source version of Molcas)

24.10

○ (2024-Nov-18)

/apl/openmolcas/v24.10/samples

23.06○ (2023-Jul-25)/apl/openmolcas/v23.06/samples
22.10○ (2023-Mar-6)/apl/openmolcas/v22.10/samples
21.10○ (2023-Mar-6)/apl/openmolcas/v21.10/samples

ORCA

(registration required)

An ab initio quantum chemistry program package

6.1.0

○ (2025-Jun-18)

(osub is available)
/apl/orca/6.1.0/samples
6.0.1○ (2024-Nov-6)(osub is available)
/apl/orca/6.0.1/samples
5.0.4○ (2023-Mar-20)(osub is available)
/apl/orca/5.0.4/samples
5.0.3○ (2022-Feb-22)(osub is available)
/apl/orca/5.0.3/samples
4.2.1○ (2020-Jan-8)(osub is available)
/apl/orca/4.2.1/samples
Parallel CONFLEX(*9)  -
ProteinMPNNSoftware for amino acid sequence prediction from a given main chain structure
 △ (2023-Oct-26)

/apl/ProteinMPNN/20231025/samples

latest code on Oct 25, 2023

PSI4Open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.
1.9.1○ (2024-Mar-5)/apl/psi4/1.9.1/samples
1.7○ (2023-Jan-30)/apl/psi4/1.7/samples
Quantum ESPRESSOIntegrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
7.5○ (2025-Sep-8)☆
CPU / GPU
/apl/qe/7.5/samples
/apl/qe/7.5-gpu/samples
7.4.1○ (2025-Feb-12)
CPU / GPU
/apl/qe/7.4.1/samples
/apl/qe/7.4.1-gpu/samples
7.4○ (2024-Feb-6)
CPU / GPU
/apl/qe/7.4/samples
/apl/qe/7.4-gpu/samples
7.3○ (2024-Feb-6)
CPU / GPU
/apl/qe/7.3/samples
/apl/qe/7.3-gpu/samples
7.2○ (2023-Apr-11)
CPU / GPU
/apl/qe/7.2/samples
/apl/qe/7.2-gpu/samples
6.8○ (2023-Jan-26)
CPU / GPU
/apl/qe/6.8/samples
/apl/qe/6.8-gpu/samples
ReactionPlusProgram to obtain the transition state and reaction path along the user’s expected reaction mechanism.
1.0○ (2018-Jan-22)/apl/reactionplus/1.0/samples
RFdiffusionAI-based Main Chain Structure Generation Software
 △ (2023-Oct-26)

/apl/RFdiffusion/20231025/samples

latest code on Oct 25, 2023

RFDiffusion AASoftware for modeling and design of various biomolecules
 △ (2024-Mar-27)

/apl/RFDiffusionAA/20240327/samples

latest code on Mar 27, 2024

SIESTAEfficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
5.2.2○ (2025-Feb-19)/apl/siesta/5.2.2/samples
5.0.1○ (2024-Jul-29)
OpenMPI / IntelMPI

/apl/siesta/5.0.1/samples
/apl/siesta/5.0.1-impi/samples

Open MPI and Intel MPI versions avail

5.0.0○ (2024-May-29)
OpenMPI / IntelMPI

/apl/siesta/5.0.0/samples
/apl/siesta/5.0.0-impi/samples

Open MPI and Intel MPI versions avail

4.1.5○ (2023-Jan-X)
MPI / OpenMP

/apl/siesta/4.1.5-mpi/samples
/apl/siesta/4.1.5-omp/samples

MPI and OpenMP versions available

TURBOMOLEOne of the fastest programs for standard quantum chemical applications.
7.9○ (2024-Dec-12)/apl/turbomole/7.9/samples
7.8.1○ (2024-Nov-12)/apl/turbomole/7.8.1/samples
7.8○ (2023-Dec-18)/apl/turbomole/7.8/samples
7.7○ (2023-Jul-18)/apl/turbomole/7.7/samples
7.6○ (2021-Dec-23)/apl/turbomole/7.6/samples
VASP(*4) (not available)-
xTBProgram for Extended Tight Binding calculation
6.7.1○ (2025/3/5)/apl/xtb/6.7.1/samples
6.7.0○ (2024/5/7)/apl/xtb/6.7.0/samples
6.5.1○ (2024/5/22)/apl/xtb/6.5.1/samples

Following GUI applications are available (X11 forwarding necessary). On Windows, you can use X11 forwarding easily with MobaXterm (WSLg, Xming, VcXsrv may also work). On mac, install and start XQuartz, and then connect via ssh with "-XY" option.

Alternatively, you can use these GUI applications on desktop of Open OnDemand (regardless of your computer's OS) using a web browser. (Please check this page to start using Open OnDemand.)

namedescription
versioncommand name / pathinstall date
GaussViewViewer for Gaussian 09 / 16.
6.1.1gview6△ (2019-Oct-29)
6.0.16/apl/gaussian/16b01/gv/gview.sh△ (2017-Feb-2)
5.0.9gview5△ (2013-Mar-13)
iMolproGUI program for Molpro
1.0.1/apl/imolpro/1.0.1/bin/imolpro-*○ (2024-Mar-8)
LuscusGUI program for Molcas/OpenMolcas
0.8.6/apl/luscus/0.8.6/bin/luscus○ (2023-Oct-4)
MoldenVisualization program of molecular and structure.
7.2.1/apl/molden/7.2.1/bin/molden○ (2023-Feb-6)
VMDMolecular graphics viewer
1.9.4 alpha
(2022/4/27)
/apl/vmd/1.9.4a57/bin/vmd○ (2023-Jan-X)
XCrySDenA crystalline and molecular structure visualisation program
1.6.2exec "module load xcrysden/1.6.2" and then
xcrysden
○ (2024-Aug-23)

○: module available
△: module not available/not necessary
☆: GPU version available

Note

(*4) We cannot install. (Licensed users can install into their directories.)
(*5) English guide for GRRM17 is available at https://afir.sci.hokudai.ac.jp/documents/manual/54. Japanese guide for this center (for GRRM14) is also available.
(*9) We cannot install ADF and Parallel CONFLEX due to their very high license fees.
(*17) You have to cite some papers when you publish papers with NTChem results. Please read official page and documentation(japanese) of NTChem.
(*21) To use CRYSTAL, license agreement is required for each user and version. CRYSTAL17 users also need to sign a new license agreement to use CRYSTAL23. Once the agreement is arrived at RCCS, you will be able to use CRYSTAL23 or/and CRYSTAL17. (CRYSTAL23 license agreement) (CRYSTAL17 license agreement)
(*22) References listed in this page must be cited when you publish results obtained with DIRAC.

Attachment Size
CRYSTAL17 license agreement 255.58 KB
CRYSTAL23 license agreement 314 KB