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Port details
protomol OO, component based, framework for molecular dynamics (MD) simulations
2.0.3_13 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port

There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 05 May 2006 20:12:57
License: GPLv2
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (117 items)
  1. /usr/local/share/licenses/protomol-2.0.3_13/catalog.mk
  2. /usr/local/share/licenses/protomol-2.0.3_13/LICENSE
  3. /usr/local/share/licenses/protomol-2.0.3_13/GPLv2
  4. bin/coords2coords
  5. bin/coulomb
  6. bin/dcd2dcd
  7. bin/iSGProtomol
  8. bin/protomol
  9. bin/xyzviz
  10. share/examples/protomol/coulomb_309/309ca.config
  11. share/examples/protomol/coulomb_309/309ca.par
  12. share/examples/protomol/coulomb_309/309ca.pos.xyz
  13. share/examples/protomol/coulomb_309/309ca.psf
  14. share/examples/protomol/alanine_dipeptide_water_184x/alanine.equil.psf
  15. share/examples/protomol/alanine_dipeptide_water_184x/alanine.7ns.namd
  16. share/examples/protomol/alanine_dipeptide_water_184x/alanine.equil.pdb
  17. share/examples/protomol/alanine_dipeptide_water_184x/ala607.pgn
  18. share/examples/protomol/alanine_dipeptide_water_184x/alanine.namd
  19. share/examples/protomol/alanine_dipeptide_water_184x/alanine.pdb
  20. share/examples/protomol/alanine_dipeptide_water_184x/alanine.psf
  21. share/examples/protomol/argon_400/argon.par
  22. share/examples/protomol/argon_400/argon.lf.conf
  23. share/examples/protomol/argon_400/argon.npt.conf
  24. share/examples/protomol/argon_400/argon.pdb
  25. share/examples/protomol/argon_400/argon.psf
  26. share/examples/protomol/argon_400/argon.vel.pdb
  27. share/examples/protomol/bpti_water_1101/bpti.par
  28. share/examples/protomol/bpti_water_1101/bpti.hmc.conf
  29. share/examples/protomol/bpti_water_1101/bpti.lf.conf
  30. share/examples/protomol/bpti_water_1101/bpti.pdb
  31. share/examples/protomol/bpti_water_1101/bpti.psf
  32. share/examples/protomol/bpti_water_1101/bpti.shmc.conf
  33. share/examples/protomol/bpti_water_14281/bpti.shake.conf
  34. share/examples/protomol/bpti_water_14281/bpti.ewald.conf
  35. share/examples/protomol/bpti_water_14281/bpti.mg.conf
  36. share/examples/protomol/bpti_water_14281/bpti.namd
  37. share/examples/protomol/bpti_water_14281/bpti.par
  38. share/examples/protomol/bpti_water_14281/bpti.pbc.conf
  39. share/examples/protomol/bpti_water_14281/bpti.pdb
  40. share/examples/protomol/bpti_water_14281/bpti.psf
  41. share/examples/protomol/butane_4/runButaneTests.sh
  42. share/examples/protomol/butane_4/README
  43. share/examples/protomol/butane_4/UA_butane.conf
  44. share/examples/protomol/butane_4/UA_butane.dhmc.conf
  45. share/examples/protomol/butane_4/UA_butane.hmc.conf
  46. share/examples/protomol/butane_4/UA_butane.lf.conf
  47. share/examples/protomol/butane_4/UA_butane.par
  48. share/examples/protomol/butane_4/UA_butane.pdb
  49. share/examples/protomol/butane_4/UA_butane.psf
  50. share/examples/protomol/butane_4/angleSetDHMC
  51. share/examples/protomol/butane_4/cleanOutput.bash
  52. share/examples/protomol/butane_4/dihedralSetDHMC
  53. share/examples/protomol/butane_4/procDihedralFile.awk
  54. share/examples/protomol/butane_4/runButaneResults.sh
  55. share/examples/protomol/alanine_dipeptide_23/ala_equil.pdb
  56. share/examples/protomol/alanine_dipeptide_23/ala_equil.psf
  57. share/examples/protomol/alanine_dipeptide_23/ala_equilibrated.pdb
  58. share/examples/protomol/alanine_dipeptide_23/ala_equilibrated.pgn
  59. share/examples/protomol/decalanine_66/dihedralIndexSet
  60. share/examples/protomol/decalanine_66/alanine.BSplineMOLLY.conf
  61. share/examples/protomol/decalanine_66/alanine.Equilibrium.conf
  62. share/examples/protomol/decalanine_66/alanine.LF.conf
  63. share/examples/protomol/decalanine_66/alanine.LFwDihedralOut.conf
  64. share/examples/protomol/decalanine_66/alanine.PLF.conf
  65. share/examples/protomol/decalanine_66/alanine.Shake.conf
  66. share/examples/protomol/decalanine_66/alanine.par
  67. share/examples/protomol/decalanine_66/alanine.pdb
  68. share/examples/protomol/decalanine_66/alanine.psf
  69. share/examples/protomol/decalanine_66/alanine.testSet
  70. share/examples/protomol/decalanine_66/alanine.water.pdb
  71. share/examples/protomol/decalanine_66/alanine.water.psf
  72. share/examples/protomol/electrons_22/22el.conf
  73. share/examples/protomol/electrons_22/22el.pos.xyz
  74. share/examples/protomol/electrons_22/22el.psf
  75. share/examples/protomol/electrons_22/22el.vel.xyz
  76. share/examples/protomol/electrons_22/el.par
  77. share/examples/protomol/methane_ethane_xxx/iSGMD_README
  78. share/examples/protomol/methane_ethane_xxx/ethane_methane.par
  79. share/examples/protomol/methane_ethane_xxx/ethane_methane.trans
  80. share/examples/protomol/methane_ethane_xxx/ethane_methane_100.conf
  81. share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.coor.xyz
  82. share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.psf
  83. share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.vel.xyz
  84. share/examples/protomol/methane_ethane_xxx/ethane_methane_100_Pure_Trappe.xsc
  85. share/examples/protomol/methane_ethane_xxx/ethane_methane_300.conf
  86. share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.coor.xyz
  87. share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.psf
  88. share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.vel.xyz
  89. share/examples/protomol/methane_ethane_xxx/ethane_methane_300_Pure_Trappe.xsc
  90. share/examples/protomol/testset/test.tcsh
  91. share/examples/protomol/testset/README
  92. share/examples/protomol/testset/hmc.Bsp_PME.pb.conf
  93. share/examples/protomol/testset/hmc.std.conf
  94. share/examples/protomol/testset/lf.Ewald.pb.conf
  95. share/examples/protomol/testset/lf.MG.conf
  96. share/examples/protomol/testset/lf.PME.pb.conf
  97. share/examples/protomol/testset/lf.std.conf
  98. share/examples/protomol/testset/lf.std.pb.conf
  99. share/examples/protomol/testset/shmc.Bsp_PME.pb.conf
  100. share/examples/protomol/testset/shmc.std.pb.conf
  101. share/examples/protomol/testset/slf.std.pb.conf
  102. share/examples/protomol/water_216/water216.vel.pdb
  103. share/examples/protomol/water_216/water216.conf
  104. share/examples/protomol/water_216/water216.coor.pdb
  105. share/examples/protomol/water_216/water216.new.pos.pdb
  106. share/examples/protomol/water_216/water216.new.vel.pdb
  107. share/examples/protomol/water_216/water216.par
  108. share/examples/protomol/water_216/water216.psf
  109. share/examples/protomol/water_648/water648.tip3.psf
  110. share/examples/protomol/water_648/water648.fluid.conf
  111. share/examples/protomol/water_648/water648.fluid.pos.xyz
  112. share/examples/protomol/water_648/water648.ice.conf
  113. share/examples/protomol/water_648/water648.ice.nvt.conf
  114. share/examples/protomol/water_648/water648.ice.pos.xyz
  115. share/examples/protomol/water_648/water648.spce.par
  116. share/examples/protomol/water_648/water648.spce.psf
  117. share/examples/protomol/water_648/water648.tip3.par
  118. Collapse this list.

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

PKGNAME: protomol

distinfo:

SHA256 (protomol-2.0.3-tar.gz) = 52c5faf69c717516a2b071dabbaed089ae7e9944b706e391e74604946a69c183
SIZE (protomol-2.0.3-tar.gz) = 2391568


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. xmu.pc : x11-toolkits/libXmu
  2. xt.pc : x11-toolkits/libXt
  3. sm.pc : x11/libSM
  4. ice.pc : x11/libICE
  5. xext.pc : x11/libXext
  6. x11.pc : x11/libX11
  7. xi.pc : x11/libXi
Runtime dependencies:
  1. xmu.pc : x11-toolkits/libXmu
  2. xt.pc : x11-toolkits/libXt
  3. sm.pc : x11/libSM
  4. ice.pc : x11/libICE
  5. xext.pc : x11/libXext
  6. x11.pc : x11/libX11
  7. xi.pc : x11/libXi
Library dependencies:
  1. libpng.so : graphics/png
  2. libtiff.so : graphics/tiff
  3. libjpeg.so : graphics/jpeg-turbo
  4. libglut.so : graphics/freeglut
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for protomol-2.0.3_13:
     EXAMPLES=on: Build and/or install examples
     GLUT=on: OpenGL Utility Toolkit support
===> Use 'make config' to modify these settings

USES:
jpeg

Master Sites:
  1. http://cytranet.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  2. http://downloads.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  3. http://excellmedia.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  4. http://freefr.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  5. http://jaist.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  6. http://kent.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  7. http://nchc.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  8. http://netcologne.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  9. http://netix.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  10. http://superb-dca2.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  11. http://superb-sea2.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  12. http://ufpr.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  13. http://vorboss.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  14. https://cytranet.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  15. https://downloads.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  16. https://excellmedia.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  17. https://freefr.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  18. https://jaist.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  19. https://kent.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  20. https://nchc.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  21. https://netcologne.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  22. https://netix.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  23. https://superb-dca2.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  24. https://superb-sea2.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  25. https://ufpr.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/
  26. https://vorboss.dl.sourceforge.net/project/protomol/ProtoMol/2.0.3/

Number of commits found: 35

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 May 2017 05:03:16
Original commit files touched by this commit  2.0.3_13
Revision:441503
rezny search for other commits by this committer
Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845
18 Dec 2016 05:34:42
Original commit files touched by this commit  2.0.3_12
Revision:428835
marino search for other commits by this committer
biology/protomol: Support build with C++11 (taken from dports)
01 Apr 2016 13:29:17
Original commit files touched by this commit  2.0.3_12
Revision:412344
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
19 Aug 2015 13:30:00
Original commit files touched by this commit  2.0.3_12
Revision:394778  Sanity Test Failure
mat search for other commits by this committer
Convert ports to use the options helpers in categories [abc]*, and minor fixes.

Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3412?
25 Jun 2015 09:32:19
Original commit files touched by this commit  2.0.3_12
Revision:390543
amdmi3 search for other commits by this committer
- Add LICENSE
- Fix shebangs

Approved by:	porgmgr (bapt)
23 Jun 2015 06:58:20
Original commit files touched by this commit  2.0.3_11
Revision:390356
bapt search for other commits by this committer
Convert to COPYTREE_SHARE
Use options helpers
22 Jun 2015 18:33:22
Original commit files touched by this commit  2.0.3_11
Revision:390310
antoine search for other commits by this committer
Convert to USES=jpeg
11 May 2015 18:34:58
Original commit files touched by this commit  2.0.3_11
Revision:386097
mat search for other commits by this committer
Cleanup DIST* variables.

When appropriate:
- Try to use DISTVERSION{SUF,PRE}FIX
- Replace PORTNAME-PORTVERSION by DISTNAME
- Convert MASTER_SITES to use macros
- Other light cleanup

With hat:	portmgr
Sponsored by:	Absolight
25 Dec 2014 20:54:43
Original commit files touched by this commit  2.0.3_11
Revision:375598
bapt search for other commits by this committer
Bump portrevision after png update
25 Dec 2014 19:04:27
Original commit files touched by this commit  2.0.3_10
Revision:375594
antoine search for other commits by this committer
Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade
20 Oct 2014 07:10:48
Original commit files touched by this commit  2.0.3_10
Revision:371237
bapt search for other commits by this committer
Cleanup plist
10 Sep 2014 20:50:37
Original commit files touched by this commit  2.0.3_10
Revision:367888
gerald search for other commits by this committer
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)
25 Aug 2014 17:19:31
Original commit files touched by this commit  2.0.3_9
Revision:366104
amdmi3 search for other commits by this committer
- Stagify
- Fix build
23 Jul 2014 16:44:28
Original commit files touched by this commit  2.0.3_9
Revision:362705
bapt search for other commits by this committer
Reset maintainership for ports not staged with no pending PR

With hat:	portmgr
16 Apr 2014 18:28:50
Original commit files touched by this commit  2.0.3_9
Revision:351411
zeising search for other commits by this committer
The FreeBSD x11@ and graphics team proudly presents
a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
(Only the first 15 lines of the commit message are shown above View all of this commit message)
15 Jan 2014 22:51:26
Original commit files touched by this commit  2.0.3_8
Revision:339845
bapt search for other commits by this committer
Reduce over inclusion of bsd.port.mk
11 Dec 2013 14:43:51
Original commit files touched by this commit  2.0.3_8
Revision:336171
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
20 Sep 2013 15:55:44
Original commit files touched by this commit  2.0.3_8
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
18 Mar 2013 06:54:40
Original commit files touched by this commit  2.0.3_8
Revision:314531
jgh search for other commits by this committer
- adoption of optionsNG
- trim historical header
- fix mixture of DOCS/EXAMPLES -> EXAMPLES
- add shared description for GLUT to bodm

Approved by:	portmgr (miwi)
04 Aug 2012 22:52:04
Original commit files touched by this commit  2.0.3_8
kwm search for other commits by this committer
Switch from libglut to freeglut and retire libglut. Libglut hasn't been
developed in years and has been dropped from the MESA 8.0 distribution.
Freeglut is a rewrite of glut and is actively developed and is used by
many linux distributions instead of libglut.

Bump all ports that directly depend on libglut because of the shlib version
change.

There are some extra items in this patch.

*) Because freeglut doesn't have the same dependancies as libglut, some ports
	need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
	with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
	remains now.
*) While here fix a png related build issue games/vegastrike.

Thanks to miwi for running the exp-run.

Approved by:	portmgr (miwi)

Collaboration with:	zeising@
Obtained from:	xorg-dev staging area.
01 Jun 2012 05:26:28
Original commit files touched by this commit  2.0.3_7
dinoex search for other commits by this committer
- update png to 1.5.10
23 Sep 2011 22:26:39
Original commit files touched by this commit  2.0.3_6
amdmi3 search for other commits by this committer
- 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
19 Mar 2011 12:38:54
Original commit files touched by this commit  2.0.3_6
miwi search for other commits by this committer
- Get Rid MD5 support
28 Mar 2010 06:47:48
Original commit files touched by this commit  2.0.3_6
dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
05 Feb 2010 11:46:55
Original commit files touched by this commit  2.0.3_5
dinoex search for other commits by this committer
- update to jpeg-8
22 Aug 2009 00:15:15
Original commit files touched by this commit  2.0.3_4
amdmi3 search for other commits by this committer
- Switch SourceForge ports to the new File Release System: categories starting
with B,C
18 Jul 2009 11:11:29
Original commit files touched by this commit  2.0.3_4
dinoex search for other commits by this committer
- update to jpeg7
Tested by:      pav on pointyhat
23 Jan 2009 16:28:36
Original commit files touched by this commit  2.0.3_3
flz search for other commits by this committer
- 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).
25 Jul 2008 14:34:52
Original commit files touched by this commit  2.0.3_2
pav search for other commits by this committer
- 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
19 Apr 2008 17:56:05
Original commit files touched by this commit  2.0.3_2
  Sanity Test Failure
miwi search for other commits by this committer
- 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)
28 Mar 2008 19:01:48
Original commit files touched by this commit  2.0.3_2
gahr search for other commits by this committer
- Fix build with GCC 4.2

Approved by:    miwi (mentor)
25 Mar 2008 22:44:48
Original commit files touched by this commit  2.0.3_2
miwi search for other commits by this committer
- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)
02 Oct 2007 09:08:37
Original commit files touched by this commit  2.0.3_1
linimon search for other commits by this committer
Mark as broken with gcc4.2.
19 May 2007 20:32:57
Original commit files touched by this commit  2.0.3_1
flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
05 May 2006 20:09:55
Original commit files touched by this commit  2.0.3
ehaupt search for other commits by this committer
Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.

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

Number of commits found: 35

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