biology/protomol 2.0.3_16 FreeBSD

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

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
License: GPLv2
Categories: biology
Package size: 1819.3 KiB, 12183.7 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

System

Port

Version

FreeBSD

biology/protomol

2.0.3_16

DragonFly

biology/protomol

2.0.3_16

HardenedBSD

biology/protomol

2.0.3_16

GhostBSD

biology/protomol

2.0.3_16

Install

Binary package:

pkg install protomol

From the ports tree:

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

To depend on this port in another port's Makefile:

RUN_DEPENDS=	protomol>0:biology/protomol

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

2.0.3_16

2.0.3_14

2.0.3_16

FreeBSD:14:quarterly

2.0.3_16

n/a

2.0.3_16

FreeBSD:15:latest

2.0.3_16

n/a

2.0.3_16

FreeBSD:15:quarterly

2.0.3_16

n/a

FreeBSD:16:latest

2.0.3_16

n/a

FreeBSD:16:quarterly

n/a

Dependencies

As this port's Makefile names them.

Library 2

libpng.so : graphics/png
libtiff.so : graphics/tiff

The full lists below include those, and their dependencies in turn.

Build dependencies 26

Run dependencies 26

No port depends on this one.

Configuration

Options name: biology_protomol

Option

Default

Description

EXAMPLES

off

Build and/or install examples

GLUT

OpenGL Utility Toolkit support

USES: jpeg shebangfix xorg
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

Files

pkg-plist 114

bin/coords2coords
bin/coulomb
bin/dcd2dcd
bin/iSGProtomol
bin/protomol
bin/xyzviz
share/examples/protomol/coulomb_309/309ca.config
share/examples/protomol/coulomb_309/309ca.par
share/examples/protomol/coulomb_309/309ca.pos.xyz
share/examples/protomol/coulomb_309/309ca.psf
share/examples/protomol/alanine_dipeptide_water_184x/alanine.equil.psf
share/examples/protomol/alanine_dipeptide_water_184x/alanine.7ns.namd
share/examples/protomol/alanine_dipeptide_water_184x/alanine.equil.pdb
share/examples/protomol/alanine_dipeptide_water_184x/ala607.pgn
share/examples/protomol/alanine_dipeptide_water_184x/alanine.namd
share/examples/protomol/alanine_dipeptide_water_184x/alanine.pdb
share/examples/protomol/alanine_dipeptide_water_184x/alanine.psf
share/examples/protomol/argon_400/argon.par
share/examples/protomol/argon_400/argon.lf.conf
share/examples/protomol/argon_400/argon.npt.conf
share/examples/protomol/argon_400/argon.pdb
share/examples/protomol/argon_400/argon.psf
share/examples/protomol/argon_400/argon.vel.pdb
share/examples/protomol/bpti_water_1101/bpti.par
share/examples/protomol/bpti_water_1101/bpti.hmc.conf
share/examples/protomol/bpti_water_1101/bpti.lf.conf
share/examples/protomol/bpti_water_1101/bpti.pdb
share/examples/protomol/bpti_water_1101/bpti.psf
share/examples/protomol/bpti_water_1101/bpti.shmc.conf
share/examples/protomol/bpti_water_14281/bpti.shake.conf
share/examples/protomol/bpti_water_14281/bpti.ewald.conf
share/examples/protomol/bpti_water_14281/bpti.mg.conf
share/examples/protomol/bpti_water_14281/bpti.namd
share/examples/protomol/bpti_water_14281/bpti.par
share/examples/protomol/bpti_water_14281/bpti.pbc.conf
share/examples/protomol/bpti_water_14281/bpti.pdb
share/examples/protomol/bpti_water_14281/bpti.psf
share/examples/protomol/butane_4/runButaneTests.sh
share/examples/protomol/butane_4/README
share/examples/protomol/butane_4/UA_butane.conf
share/examples/protomol/butane_4/UA_butane.dhmc.conf
share/examples/protomol/butane_4/UA_butane.hmc.conf
share/examples/protomol/butane_4/UA_butane.lf.conf
share/examples/protomol/butane_4/UA_butane.par
share/examples/protomol/butane_4/UA_butane.pdb
share/examples/protomol/butane_4/UA_butane.psf
share/examples/protomol/butane_4/angleSetDHMC
share/examples/protomol/butane_4/cleanOutput.bash
share/examples/protomol/butane_4/dihedralSetDHMC
share/examples/protomol/butane_4/procDihedralFile.awk
share/examples/protomol/butane_4/runButaneResults.sh
share/examples/protomol/alanine_dipeptide_23/ala_equil.pdb
share/examples/protomol/alanine_dipeptide_23/ala_equil.psf
share/examples/protomol/alanine_dipeptide_23/ala_equilibrated.pdb
share/examples/protomol/alanine_dipeptide_23/ala_equilibrated.pgn
share/examples/protomol/decalanine_66/dihedralIndexSet
share/examples/protomol/decalanine_66/alanine.BSplineMOLLY.conf
share/examples/protomol/decalanine_66/alanine.Equilibrium.conf
share/examples/protomol/decalanine_66/alanine.LF.conf
share/examples/protomol/decalanine_66/alanine.LFwDihedralOut.conf
share/examples/protomol/decalanine_66/alanine.PLF.conf
share/examples/protomol/decalanine_66/alanine.Shake.conf
share/examples/protomol/decalanine_66/alanine.par
share/examples/protomol/decalanine_66/alanine.pdb
share/examples/protomol/decalanine_66/alanine.psf
share/examples/protomol/decalanine_66/alanine.testSet
share/examples/protomol/decalanine_66/alanine.water.pdb
share/examples/protomol/decalanine_66/alanine.water.psf
share/examples/protomol/electrons_22/22el.conf
share/examples/protomol/electrons_22/22el.pos.xyz
share/examples/protomol/electrons_22/22el.psf
share/examples/protomol/electrons_22/22el.vel.xyz
share/examples/protomol/electrons_22/el.par
share/examples/protomol/methane_ethane_xxx/iSGMD_README
share/examples/protomol/methane_ethane_xxx/ethane_methane.par
share/examples/protomol/methane_ethane_xxx/ethane_methane.trans
share/examples/protomol/methane_ethane_xxx/ethane_methane_100.conf
share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.coor.xyz
share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.psf
share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.vel.xyz
share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.xsc
share/examples/protomol/methane_ethane_xxx/ethane_methane_300.conf
share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.coor.xyz
share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.psf
share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.vel.xyz
share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.xsc
share/examples/protomol/testset/test.tcsh
share/examples/protomol/testset/README
share/examples/protomol/testset/hmc.Bsp_PME.pb.conf
share/examples/protomol/testset/hmc.std.conf
share/examples/protomol/testset/lf.Ewald.pb.conf
share/examples/protomol/testset/lf.MG.conf
share/examples/protomol/testset/lf.PME.pb.conf
share/examples/protomol/testset/lf.std.conf
share/examples/protomol/testset/lf.std.pb.conf
share/examples/protomol/testset/shmc.Bsp_PME.pb.conf
share/examples/protomol/testset/shmc.std.pb.conf
share/examples/protomol/testset/slf.std.pb.conf
share/examples/protomol/water_216/water216.vel.pdb
share/examples/protomol/water_216/water216.conf

The first 100 are listed.

distinfo 1

File

Size

SHA256

protomol-2.0.3-tar.gz

2.391568e+06

52c5faf69c717516a2b071dabbaed089ae7e9944b706e391e74604946a69c183

Master sites 1

SF/protomol/ProtoMol/2.0.3

Commit history 0

No commits in the history this site was built from.