Package Programs List (Molecular Science)

Last update: May 2, 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 SDK25.3module: nvhpc/25.3, nvhpc/25.3-byo, nvhpc/25.3-nompi
24.9module: nvhpc/24.9, nvhpc/24.9-byo, nvhpc/24.9-nompi
24.3module: nvhpc/24.3, nvhpc/24.3-byo, nvhpc/24.3-nompi
23.9module: nvhpc/23.9, nvhpc/23.9-byo, nvhpc/23.9-nompi
23.5module: nvhpc/23.5, nvhpc/23.5-byo, nvhpc/23.5-nompi
22.11module: nvhpc/22.11, nvhpc/22.11-byo, nvhpc/22.11-nompi
Intel oneAPI Compiler Runtime [2]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 MKL2025.1.0, 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 MPI2021.15, 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)
CUDA12.8 Update 1module: cuda/12.8u1
12.6 Update 2module: cuda/12.6u2
12.4 Update 1module: cuda/12.4u1
12.2 Update 2*module: 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 MPI5.0.6, 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.

namedescription
versioninstall datenote
ABClusterSoftware for cluster structure optimization and conformation search
3.0○ (2023-Nov-28) 
ABINIT-MPA software for fast Fragment-Molecular-Orbital (FMO) calculations.
v2r8○ (2025-Jan-7) 
v2r4○ (2023-Feb-21) 
v1r22○ (2023-Feb-21) 
ADF(*9) (not available) 

AlphaFold

(version3)
(version2)

AI program for predictions of protein structure.
3.0.0
(Jan 16, 2025)
△ (2025-Jan-16)GPU is required for inference.
AlphaFold3 model parameters must be requested and downloaded by the user themselves.
3.0.0
(Nov 26, 2024)
△ (2024-Nov-26)
2.3.2△ (2024-Feb-8) 
2.3.1△ (2023-Feb-6) 
2.2.0△ (2022-Mar-14) 
2.1.1△ (2021-Nov-8) 
2.1.0△ (X-X-X) 
2.0.0 (2021/8/19)△ (2021-Aug-23) 
2.0.0 (2021/7/20)△ (2021-Jul-26) 
AmberPackage of molecular simulation programs.
24-update3○ (2025-Mar-6)There is a note on "module" command.
Please check notes of installation details.
(AmberTools24-update8)
24-update1○ (2024-Jun-11)(AmberTools24-update2)
22-update4○ (2023-Aug-25)(Ambertools23-update4)
22-update1○ (2023-Jan-X)(AmberTools22-update4)
20-update13○ (2023-Jan-X)(built with configure)
AutoDockAutomated docking tools
4.2.6○ (2023-Nov-24) 
AutoDock-GPUGPU-enabled version of AutoDock
1.5.3○ (2023-Nov-24) 
AutoDock VinaImproved version of AutoDock
1.2.5○ (2023-Nov-24) 
CENSOProgram for evaluating structure ensembles at DFT level. 
2.1.3○ (2025-May-1)anmr from ENSO 2.0.2 was added manually.
1.2.0○ (2024-May-22)(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) 

CP2K

A quantum chemistry and solid state physics software package.

2024.3

○ (2024-Oct-24)

 

2024.2

○ (2024-Aug-22)

 
2023.1

○ (2023-Apr-6)

 
9.1

○ (2023-Jan-X)

 
CRESTA program for the automated exploration of the low-energy molecular chemical space.
3.0.1○ (2024-May-21) 
CRYSTALGeneral-purpose programs for the study of crystalline solids.
23-1.0.1○ (2024-Jul-19)(*21)
17-1.0.2○ (2023-Jan-X)
DaltonQuantum chemistry software capable of calculating various molecular properties
2020.1○ (2024-Nov-8) 
DFTB+Fast and efficient versatile quantum mechanical simulation software package
23.1○ (2023-Jul-19)
MPI / OpenMP
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) 
19.0○ (2023-Jan-27) 

GAMESS

General atomic and molecular electronic structure system.
2024-R2(Jul15)○ (2024-Oct-31)(NBO 7.0.10 enabled)
2023-R2(Sep30)○ (2023-Dec-7)(NBO 7.0.10 enabled)
2022-R2(Sep30)○ (2023-Jan-X)(NBO 7.0.7 enabled)
2021-R1(Jun30)○ (2023-Jan-X)(NBO 7.0.7 enabled)
GaussianAb initio molecular orbital calculations.
16.C.02○ (2022-Mar-14)(NBO 7.0.10 enabled)
16.C.01○ (2019-Aug-2)(NBO 7.0.10 enabled)
16.B.01○ (2018-Mar-12) 
09.E.01○ (2015-Dec-24) 
GENESISMolecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes.
2.1.4○ (2025-Jan-10)
CPU / GPU
 
2.1.2○ (2024-Jan-16)
CPU / GPU
 
2.0.3○  (2023-Jan-X)
CPU / GPU
 
GROMACSFast, Free and Flexible MD
2024.5○ (2025-Jan-27)
CPU / GPU
 
2024.4○ (2024-Nov-5)
CPU / GPU
 
2024.2○ (2024-May-16)
CPU / GPU
 
2023.5○ (2024-May-7)
CPU / GPU
 
2023.4○ (2024-Jan-26)
CPU / GPU
 
2023.2○ (2023-Aug-9)
CPU / GPU
 
2022.6○ (2023-Jul-12)
CPU / GPU
 
2022.4○ (2023-Jan-X)
CPU / GPU
 
2021.7○ (2023-Apr-14)
CPU / GPU
 
2021.6○ (2023-Jan-X)
CPU / GPU
 
2021.4○ (2023-Jan-X)
CPU / GPU
 
GRRMAutomated Exploration of Reaction Pathways.
23〇 (2024-Jan-11)

Application is required for use.

(multinode parallel available)

17(*5)(2021-Jan-27)(multinode parallel available)
14○ (2015-Jul-29) 
LAMMPSLarge-scale Atomic/Molecular Massively Parallel Simulator.
29Aug2024 Update 2○ (2025-Apr-18)
CPU(GCC,Intel) / GPU
 
29Aug2024 Update 1○ (2025-Feb-21)
CPU(GCC,Intel) / GPU
 
29Aug2024○ (2024-Sep-6)
CPU(GCC,Intel) / GPU
 
2Aug23○ (2023-Oct-16)
CPU(GCC,Intel) / GPU
Intel MPI
23Jun22 Update 2○ (2023-Jan-X)
CPU / GPU
(netcdf off)
○ (2023-Apr-18)
CPU / GPU
Intel MPI
29Sep21 Update 3○ (2023-Apr-18)
CPU / GPU
Intel MPI
29Sep21○ (2023-Jan-X)
CPU / GPU
(netcdf off)
LigandMPNNSoftware for designing sequences that bind to small ligands
 △ (2024-Mar-27)latest code on Mar 27, 2024

Molpro(*2)

Complete system of ab initio programs.

2025.1.0

△ (2025-Mar-14)

 
2024.3.0△ (2024-Nov-15) 
2024.2.0△ (2024-Sep-9) 
2024.1.0△ (2024-Mar-11) 
2023.2.0△ (2023-Oct-11) 
2023.1.0△ (2023-Sep-19) 
2022.3.0△ (2023-Jan-X)(HPC-X)
△ (2023-May-18)(MVAPICH)
2022.2.2△ (2023-Jan-X) 
2021.3.1△ (2023-May-10) 
2015.1-44△ (2023-Jan-X) 
NAMDScalable molecular dynamics program.
3.0.1○ (2024-Oct-31)
MPI / SMP / SMP+CUDA
 
3.0○ (2024-Jul-5)
MPI / SMP / SMP+CUDA
 
3.0b7○ (2024-May-23)
MPI / SMP / SMP+CUDA
 
3.0b6○ (2024-Mar-6)
MPI / SMP / SMP+CUDA
 
3.0b2○ (2023-Apr-10)(GPU version only)
2.14○ (2023-Jan-X)
CPU / GPU
 
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) 
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
 
7.2.2○ (2024-Mar-5)
CPU / GPU
 
7.0.2○ (2023-Mar-6) 
6.8○ (2023-Mar-6)for ReactionPlus
OmegaFoldA Protein Structure Prediction Software
1.1.0○ (2024-Jun-12) 

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) 
8.1.0○ (2023-Dec-5) 

OpenMolcas

Quantum chemistry software. (Open source version of Molcas)

24.10

○ (2024-Nov-18)

 

23.06○ (2023-Jul-25) 
22.10○ (2023-Mar-6) 
21.10○ (2023-Mar-6) 
ORCAAn ab initio quantum chemistry program package
6.0.1○ (2024-Nov-6)(registration required)
5.0.4○ (2023-Mar-20)
5.0.3○ (2022-Feb-22)
4.2.1○ (2020-Jan-8)
Parallel CONFLEX(*9)   
ProteinMPNNSoftware for amino acid sequence prediction from a given main chain structure
 △ (2023-Oct-26)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) 
1.7○ (2023-Jan-30) 
Quantum ESPRESSOIntegrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
7.4.1○ (2024-Feb-12)
CPU / GPU
 
7.4○ (2024-Feb-6)
CPU / GPU
 
7.3○ (2024-Feb-6)
CPU / GPU
 
7.2○ (2023-Apr-11)
CPU / GPU
 
6.8○ (2023-Jan-26)
CPU / GPU
 
ReactionPlusProgram to obtain the transition state and reaction path along the user’s expected reaction mechanism.
1.0○ (2018-Jan-22) 
RFdiffusionAI-based Main Chain Structure Generation Software
 △ (2023-Oct-26)latest code on Oct 25, 2023
RFDiffusion AASoftware for modeling and design of various biomolecules
 △ (2024-Mar-27)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) 
5.0.1○ (2024-Jul-29)
OpenMPI / IntelMPI
Open MPI and Intel MPI versions avail
5.0.0○ (2024-May-29)
OpenMPI / IntelMPI
Open MPI and Intel MPI versions avail
4.1.5○ (2023-Jan-X)
MPI / OpenMP
MPI and OpenMP versions available
TURBOMOLE(*3)One of the fastest programs for standard quantum chemical applications.
7.9○ (2024-Dec-12) 
7.8.1○ (2024-Nov-12) 
7.8○ (2023-Dec-18) 
7.7○ (2023-Jul-18) 
7.6○ (2021-Dec-23) 
VASP(*4) (not available) 
xTBProgram for Extended Tight Binding calculation
6.7.1○ (2025/3/5) 
6.7.0○ (2024/5/7) 
6.5.1○ (2024/5/22) 

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.

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

(*2) molpro license will be expired on Sep 15, 2025. The license will be renewed every year.
(*3) Only non-commercial users in Japan can use this. The license will be expired in Feb, 2026. The license will be renewed every year.
(*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 fee.

(*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