Port details |
- protomol OO, component based, framework for molecular dynamics (MD) simulations
- 2.0.3_14 biology
=0 2.0.3_14Version of this port present on the latest quarterly branch. - 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
 - Port Added: 2006-05-05 20:12:57
- Last Update: 2021-04-06 14:31:07
- Commit Hash: 305f148
- License: GPLv2
- 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.
WWW: http://protomol.sourceforge.net/
- SVNWeb : git : Homepage
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- protomol>0:biology/protomol
- To install the port:
- cd /usr/ports/biology/protomol/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/protomol
- pkg install protomol
- PKGNAME: protomol
- Flavors: there is no flavor information for this port.
- distinfo:
- SHA256 (protomol-2.0.3-tar.gz) = 52c5faf69c717516a2b071dabbaed089ae7e9944b706e391e74604946a69c183
SIZE (protomol-2.0.3-tar.gz) = 2391568
- Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- xmu.pc : x11-toolkits/libXmu
- xt.pc : x11-toolkits/libXt
- sm.pc : x11/libSM
- ice.pc : x11/libICE
- xext.pc : x11/libXext
- x11.pc : x11/libX11
- xi.pc : x11/libXi
- Runtime dependencies:
-
- xmu.pc : x11-toolkits/libXmu
- xt.pc : x11-toolkits/libXt
- sm.pc : x11/libSM
- ice.pc : x11/libICE
- xext.pc : x11/libXext
- x11.pc : x11/libX11
- xi.pc : x11/libXi
- Library dependencies:
-
- libpng.so : graphics/png
- libtiff.so : graphics/tiff
- libjpeg.so : graphics/jpeg-turbo
- 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_14:
EXAMPLES=on: Build and/or install examples
GLUT=on: OpenGL Utility Toolkit support
===> Use 'make config' to modify these settings
- Options name:
- biology_protomol
- USES:
- jpeg shebangfix xorg gl xorg
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: see SVNWeb link above for full details) |
Date | By | Description |
06 Apr 2021 14:31:07 2.0.3_14
|
Mathieu Arnold (mat)  |
Remove # $FreeBSD$ from Makefiles. |
04 Nov 2019 21:08:20
2.0.3_14
|
zeising  |
Add USES=xorg USES=gl, ports categories b
Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'. |
25 Aug 2018 03:47:25
2.0.3_14
|
tobik  |
biology/protomol: Fix doubled USES overwriting the old value
- Make sure shebangfix is actually used |
25 Aug 2018 03:45:28
2.0.3_13
|
tobik  |
biology/protomol: Fix build with Clang 6
Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream'
(aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const
basic_ostream<char>'))
*myStream << a;
~~~~~~~~~ ^ ~
/usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no
known conversion from 'const std::__1::ostream' (aka 'const
basic_ostream<char>') to 'const void *' for 1st argument; take the address of
the argument with &
basic_ostream& operator<<(const void* __p);
^
... and so on ...
http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log |
23 May 2017 05:03:16
2.0.3_13
|
rezny  |
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
2.0.3_12
|
marino  |
biology/protomol: Support build with C++11 (taken from dports) |
01 Apr 2016 13:29:17
2.0.3_12
|
mat  |
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight |
19 Aug 2015 13:30:00
2.0.3_12 
|
mat  |
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
2.0.3_12
|
amdmi3  |
- Add LICENSE
- Fix shebangs
Approved by: porgmgr (bapt) |
23 Jun 2015 06:58:20
2.0.3_11
|
bapt  |
Convert to COPYTREE_SHARE
Use options helpers |
22 Jun 2015 18:33:22
2.0.3_11
|
antoine  |
Convert to USES=jpeg |
11 May 2015 18:34:58
2.0.3_11
|
mat  |
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
2.0.3_11
|
bapt  |
Bump portrevision after png update |
25 Dec 2014 19:04:27
2.0.3_10
|
antoine  |
Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade |
20 Oct 2014 07:10:48
2.0.3_10
|
bapt  |
Cleanup plist |
10 Sep 2014 20:50:37
2.0.3_10
|
gerald  |
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
2.0.3_9
|
amdmi3  |
- Stagify
- Fix build |
23 Jul 2014 16:44:28
2.0.3_9
|
bapt  |
Reset maintainership for ports not staged with no pending PR
With hat: portmgr |
16 Apr 2014 18:28:50
2.0.3_9
|
zeising  |
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 ) |
15 Jan 2014 22:51:26
2.0.3_8
|
bapt  |
Reduce over inclusion of bsd.port.mk |
11 Dec 2013 14:43:51
2.0.3_8
|
bapt  |
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology |
20 Sep 2013 15:55:44
2.0.3_8
|
bapt  |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
18 Mar 2013 06:54:40
2.0.3_8
|
jgh  |
- 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
2.0.3_8
|
kwm  |
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
2.0.3_7
|
dinoex  |
- update png to 1.5.10 |
23 Sep 2011 22:26:39
2.0.3_6
|
amdmi3  |
- 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
2.0.3_6
|
miwi  |
- Get Rid MD5 support |
28 Mar 2010 06:47:48
2.0.3_6
|
dinoex  |
- update to 1.4.1
Reviewed by: exp8 run on pointyhat
Supported by: miwi |
05 Feb 2010 11:46:55
2.0.3_5
|
dinoex  |
- update to jpeg-8 |
22 Aug 2009 00:15:15
2.0.3_4
|
amdmi3  |
- Switch SourceForge ports to the new File Release System: categories starting
with B,C |
18 Jul 2009 11:11:29
2.0.3_4
|
dinoex  |
- update to jpeg7
Tested by: pav on pointyhat |
23 Jan 2009 16:28:36
2.0.3_3
|
flz  |
- 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
2.0.3_2
|
pav  |
- 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
2.0.3_2 
|
miwi  |
- 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
2.0.3_2
|
gahr  |
- Fix build with GCC 4.2
Approved by: miwi (mentor) |
25 Mar 2008 22:44:48
2.0.3_2
|
miwi  |
- 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
2.0.3_1
|
linimon  |
Mark as broken with gcc4.2. |
19 May 2007 20:32:57
2.0.3_1
|
flz  |
- 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
2.0.3
|
ehaupt  |
Add protomol 2.0.3, OO, component based, framework for molecular
dynamics (MD) simulations.
PR: 95123
Submitted by: Sangwoo Shim <sangwoos@gmail.com> |