Molecular software - Revision history

Wtitulaer at 15:22, 28 June 2024

2024-06-28T15:22:57Z

← Older revision		Revision as of 15:22, 28 June 2024
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	\|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		\|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		\|[[Chimera]] \|\| Molecular modelling visualization program \|\| Academic \|\| cn142
	\|-		\|-
	\|DOCK 3.8 \|\| Molecular docking of large-scale libraries (known as virtual screening). \|\| Academic, personal \|\| cn142		\|DOCK 3.8 \|\| Molecular docking of large-scale libraries (known as virtual screening). \|\| Academic, personal \|\| cn142

Wtitulaer at 12:20, 28 June 2024

2024-06-28T12:20:21Z

← Older revision		Revision as of 12:20, 28 June 2024
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	== Applying for access to the Molecular Chemistry cluster ==		== 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 [~~make link]~~ 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 we have the following running setup:~~
	~~{\| class="wikitable" style="margin:auto"~~
	~~\|+Cluster nodes of the Molecular Chemistry cluster~~
	\|-
	~~!Name of the node !! CPU !! RAM !! GPU !! Main group(s)~~
	\|-
	~~\| cn100 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm~~
	\|-
	~~\| cn101 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm~~
	\|-
	~~\| cn102 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm~~
	\|-
	~~\| cn103 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm~~
	\|-
	~~\| cn142 \|\| 2x 20-core Intel Xeon Silver 4416+ \|\| 256 GB \|\| 2x RTX A4000 \|\| molmech~~
	\|}

Wtitulaer at 11:20, 28 June 2024

2024-06-28T11:20:43Z

← Older revision		Revision as of 11:20, 28 June 2024
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	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.		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 ~~SOC~~ cluster ==		== 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 [make link] 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 [make link] Molecular Chemistry cluster.

Wtitulaer: /* (Currently) available softwares */

2024-06-28T10:39:12Z

(Currently) available softwares

← Older revision		Revision as of 10:39, 28 June 2024
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	\|-		\|-
	\|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		\|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		\|DOCK 3.8 \|\| Molecular docking of large-scale libraries (known as virtual screening). \|\| Academic, personal \|\| cn142
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	\|Gromacs \|\| Running molecular dynamics (MD) simulations of biomolecules and ligands on molecular mechanics level of theory and analyzing trajectories.		\|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 modelling, Fragment-growing, Library enumeration. Interfaces to Gaussian, AMBER, NAMD are available. \|\| Rutjes group \|\| cn142		\|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.		\|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
	\|}		\|}

Wtitulaer at 10:35, 28 June 2024

2024-06-28T10:35:13Z

← Older revision		Revision as of 10:35, 28 June 2024
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	== (Currently) available softwares ==		== (Currently) available softwares ==
	This table should list all softwares available. Should your desired software not be on the list, please contact		This table should list all softwares available. Should your desired software not be on the list, please contact wtitulaer to see what is possible.
			{\|class="wikitable" style="margin:auto"
			\|+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
			\|-
			\|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 modelling, Fragment-growing, Library enumeration. 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.
			\|-
			\|}

Wtitulaer at 10:18, 28 June 2024

2024-06-28T10:18:33Z

← Older revision		Revision as of 10:18, 28 June 2024
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	== Applying for access to the SOC cluster ==		== Applying for access to the SOC 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'''		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 [make link] Molecular Chemistry cluster.

	~~The primary group~~		Currently we have the following running setup:
			{\| class="wikitable" style="margin:auto"
	~~For more information on~~ the ~~cluster see [make link]~~ Molecular Chemistry cluster.		\|+Cluster nodes of the Molecular Chemistry cluster
			\|-
	~~We have made two groups on~~ the ~~cluster: '''~~molmech~~''': molecular mechanics, SOC members and~~		!Name of the node !! CPU !! RAM !! GPU !! Main group(s)
			\|-
			\| cn100 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn101 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn102 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn103 \|\| 1x 64-core AMD EPYC 7742 \|\| 256 GB \|\| - \|\| qm
			\|-
			\| cn142 \|\| 2x 20-core Intel Xeon Silver 4416+ \|\| 256 GB \|\| 2x RTX A4000 \|\| molmech
			\|}

	~~Access to Gaussian therefore requires contacting Jan Zelenka to be added to the~~
	~~Currently we have the following running setup:~~

	== (Currently) available softwares ==		== (Currently) available softwares ==
			This table should list all softwares available. Should your desired software not be on the list, please contact

Wtitulaer: Created page with "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'..."

2024-06-28T10:05:10Z

Created page with "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'..."

New page

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 SOC 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'''

The primary group

For more information on the cluster see [make link] Molecular Chemistry cluster.

We have made two groups on the cluster: '''molmech''': molecular mechanics, SOC members and

Access to Gaussian therefore requires contacting Jan Zelenka to be added to the
Currently we have the following running setup:

== (Currently) available softwares ==