Molecular software

The SOC has access to a variety of chemistry related softwares. Some of these come with paid licenses however as well as some requiring hardware the general user laptop doesn't have. Therefore, the SOC has a dedicated computing cluster running under maintenance by C&Cz and has a computer workstation where visual programmes can more easily be ran from. This page serves as a guide how to get access to these systems as well as providing an overview of the lab's current running softwares.

Applying for access to the SOC workstation

Application for the SOC-workstation requires sending an email to socmoe-access@science.ru.nl, after which you will receive a document[make link] to read prior to accessing the workstation. It should be stressed that due to paid licences to Floris's name, people outside the SOC who still would like to use the machine will have to add Floris to their list of authors upon publication.

Applying for access to the Molecular Chemistry cluster

The SOC cluster shares its computing power with the spectroscopy and catalysis group from Jana Roithova. In order to get access you first need a science account with which you can access the lilo login server (more details on: https://cncz.science.ru.nl/nl/howto/ssh/). Afterwards you need to be added to the group molmech before you can access cn142 (the main SOC cluster node), which is currently governed by wtitulaer. More information on using the cluster node can be found at Molecular chemistry cluster.

(Currently) available softwares

This table should list all softwares available. Should your desired software not be on the list, please contact wtitulaer to see what is possible.

Software available on the Molecular Chemistry cluster

Software	Usual purpose(s)	License-type	Nodes installed
AMBER24	Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory, analyzing trajectories and performing other protein-ligand modelling tasks	Academic, personal	cn142
CHARMM	Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory, performing protein-ligand modelling tasks	Academic, personal	cn103, cn142
Chimera	Molecular modelling visualization program	Academic	cn142
DOCK 3.8	Molecular docking of large-scale libraries (known as virtual screening).	Academic, personal	cn142
Gaussian	Small molecule calculations on DFT level of theory such as geometry optimizations and predicting IR-spectra from these.
GOLD	More precise molecular docking via genetic algorithm (GA) pose sampling	Academic, RU-broad from solid state chemistry	cn142(?)
Gromacs	Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory and analyzing trajectories.
MOE	Variety of medicinal chemistry related operations such as: QSAR, Pharmacophores, Homology Modelling, (template-based) Docking, Protein-ligand modelling, Fragment-growing, Library enumeration, Visualization program. Interfaces to Gaussian, AMBER, NAMD are available.	Rutjes group	cn142
NAMD	Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory.
YASARA Structure	Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program	Academic wtitulaer personal	cn142