biology/protomol 2.0.3_16 DragonFly

OO, component based, framework for molecular dynamics (MD) simulations

System: DragonFly
Repository: DPorts
Maintainer: [email protected] (as in FreeBSD)
License: GPLv2
Categories: biology
Package size: 1818.6 KiB, 13121.6 KiB installed

Description

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping is used to improve long-term efficiency. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators. In addition, ProtoMol has been designed to interact with VMD, a visualization engine developed by the University of Illinois that is used for displaying large biomolecular systems in three dimensions. ProtoMol is freely distributed software, and the source code is available.

In the other systems

The newest version among them is 2.0.3, as upstream numbers it.

System

Port

Version

Vulnerabilities

Status

Maintainer

Last update

DragonFly

biology/protomol

2.0.3_16 newest

none known

[email protected]

FreeBSD

biology/protomol

2.0.3_16 newest

none known

[email protected]

HardenedBSD

biology/protomol

2.0.3_16 newest

no data

[email protected]

GhostBSD

biology/protomol

2.0.3_16 newest

no data

[email protected]

Install

Binary package:

pkg install protomol

From DPorts:

cd /usr/dports/biology/protomol && make install clean

Dependency graph

Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.

graph LR
  me["biology/protomol"]
  me --> d0["graphics/freeglut"]
  me --> d1["graphics/jpeg-turbo"]
  me --> d2["graphics/png"]
  me --> d3["graphics/tiff"]
  me --> d4["x11-toolkits/libXmu"]
  me --> d5["x11-toolkits/libXt"]
  me --> d6["x11/libICE"]
  me --> d7["x11/libSM"]
  me -.-> dmore(["3 more"])
  classDef this fill:#ab2b28,color:#ffffff,stroke:#ab2b28
  class me this

Dependencies

Run dependencies 11

No port depends on this one.

Configuration

No options to configure.

Service scripts: none

Message after installing

===>   NOTICE:

The protomol port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing