protomol 2.0.3_6 biology =0

OO, component based, framework for molecular dynamics (MD) simulations
Maintained by: sangwoos@gmail.com
Port Added: 05 May 2006 20:12:57
License: not specified in port

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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.

WWW: http://protomol.sourceforge.net/

CVSWeb : Sources : Main Web Site : Distfiles Availability : PortsMon

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NOTE: FreshPorts displays only required dependencies information. Optional dependencies are not covered.
Required Libraries: graphics/png, graphics/jpeg, graphics/tiff, graphics/libglut
There are no ports dependent upon this port

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To install the port: cd /usr/ports/biology/protomol/ && make install clean
To add the package: pkg_add -r protomol

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Configuration Options

===> The following configuration options are available for protomol-2.0.3_6:
     GLUT=on (default) "Use glut"
===> Use 'make config' to modify these settings

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Master Sites:

http://heanet.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://sunet.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://iweb.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://switch.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://surfnet.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://kent.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://freefr.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://voxel.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://jaist.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://osdn.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://nchc.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://ncu.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://transact.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://softlayer.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://internode.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://ufpr.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

http://waix.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

ftp://ftp.FreeBSD.org/pub/FreeBSD/ports/distfiles/

- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS)
- Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead

PR:             157936
Submitted by:   myself
Exp-runs by:    pav
Approved by:    pav

- Get Rid MD5 support

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- update to jpeg-8

- Switch SourceForge ports to the new File Release System: categories starting
with B,C

- update to jpeg7
Tested by:      pav on pointyhat

- Update X.org ports to 7.4+ (few ports are more recent than the katamari).
- Bump PORTREVISION for all ports depending on libglut since the shlib
version number went from 4 to 3.
- Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't
installed anymore.
- Couple of ports fixes (mostly missing xorg components added to USE_XORG).

- Remove USE_GCC where it can be satisfied with base compiler on following
  FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT

- Remove unneeded dependency from gtk12/gtk20 [1]
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Remove X11BASE support in favor of LOCALBASE or PREFIX
- Use USE_LDCONFIG instead of INSTALLS_SHLIB
- Remove unneeded USE_GCC 3.4+

Thanks to all Helpers:
        Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr,
        ehaupt, nox, itetcu, flz, pav

PR:             116263
Tested on:      pointyhat
Approved by:    portmgr (pav)

- Fix build with GCC 4.2

Approved by:    miwi (mentor)

- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)

Mark as broken with gcc4.2.

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.

PR:             95123
Submitted by:   Sangwoo Shim <sangwoos@gmail.com>

12 vulnerabilities affecting 17 ports have been reported in the past 14 days

^* - modified, not new

All vulnerabilities