Package Details: gromacs 2024.4-2

Git Clone URL: https://aur.archlinux.org/gromacs.git (read-only, click to copy)
Package Base: gromacs
Description: A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Upstream URL: http://www.gromacs.org/
Keywords: chemistry science simulations
Licenses: LGPL-2.1-only
Submitter: xyproto
Maintainer: hseara (vedranmiletic)
Last Packager: vedranmiletic
Votes: 23
Popularity: 0.000003
First Submitted: 2011-12-14 17:03 (UTC)
Last Updated: 2024-11-08 05:39 (UTC)

Dependencies (14)

Required by (1)

Sources (1)

Latest Comments

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duca commented on 2013-04-26 03:06 (UTC)

Sorry for the delay

hseara commented on 2013-04-18 15:19 (UTC)

Hi, it is the second time I put out of date the package. Please update it.

<deleted-account> commented on 2013-04-08 08:34 (UTC)

Hi, after running into some problems like missing permission to edit /pkg and folders getting created to early, i had to modify the PKGBUILD. If anyone has similar problems, maybe this can help: http://codepad.org/gmVjykgp This is my first PKGBUILD, so please tell me if something could be done better.

quizzmaster commented on 2012-11-24 23:30 (UTC)

May you add the fix for usind do_dssp with last dssp version? Thats the way i did it: git clone git://git.gromacs.org/gromacs.git git checkout --track -b release-4-5-patches origin/release-4-5-patches

duca commented on 2012-05-14 19:52 (UTC)

@josephgbr Thanks for sharing the new completion directory. hseara added ckame to makedepends completion.* is there due to gromacs dev discretion but the new package will remove them (it was like this a awhile ago). @hseara a) I got your point, i misread your previous pkgbuild. b) I had this problem a while ago and never and never tried again using n>4. c) This is not my assumption, it's an upstream assumption (just check your /etc/profile.d and you'll see only .csh and .sh files in there). I dont mind moving all GMXRC.* scripts to that location (and patch GMXRC to updated location of GMXRC.*) and let /usr/bin with only gromacs executables At first i thought you were just having your time because of my comments on your package, but i do not think like this anymore. Actually i appreciate your comments, they help me improve the quality of my packages in the end.

hseara commented on 2012-05-12 08:45 (UTC)

Here is the new PKGBUILD with cmake in makedepends http://codepad.org/VLnCPrEJ PD: Our packages have been already merged

rafaelff commented on 2012-05-12 08:01 (UTC)

Some comments on this package: * 'cmake' is missing in makedepends. * if you decide to use doxygen, then add it to makedepends as well * 'bash-completion' directory changed to /usr/share/bash-completion/completions/ (WTH is /usr/bin/completion.* doing in /usr/bin ?)

hseara commented on 2012-05-12 00:42 (UTC)

I will try to answer in order: a) No you are wrong you don't need two copies. Cmake copies everything you need to the single and double directory. Please realize that you make make installs in them. Please read carefully the PKGBUILD I sent you because I have the feeling you did not understand the point. Moreover, I have tested it and it works perfectly. If not please let me know what is the problem. b) Regarding -j2, David van der Spoel, Ph.D. one of the main gromacs developer compiles gromacs with 32 cores, at least it is what he always says. Myself I have always, more than 10 years, compile with the maximum amount of cores and I have never seen a problem. If you see any problem please fill a bug report upstream as it is really an important issue that no one I know so far has encounter. So unless you can backup your claim you should definitely remove "-j2". c) Regarding GMXRC. You are assuming that everybody uses bash as a main interpreter. It is very likely that you are right but it might not be the case. The beauty of sourcing in /etc/profile.d/GMXRC is that it will select the appropriated script for the used interpreter. By the way be aware that this files are changed in the compilation to match the installation paths. That's why I use the move command. So I do not understand the problem you expose, but if you know any other better way to do the same I do not have any problem. d) Yes, we definitely need to merge this two packages. I will ask the merge tomorrow. Thanks, and please do not see in my comments any bad intentions. I just want to help to have the best package for everybody.

duca commented on 2012-05-11 14:56 (UTC)

Strange, the suffixes in this release are definatelly a typo for the first thing i did was to remove them all. I believe while i was adding the comments i brought them back. Aesthetically i agree that the cleaner the better, not many packages out there are clean in the sense of number of lines nor in their solutions to correctly build their packages. If you follow the discussion list you have alredy read some debate. But in this case if you run cmake (and make) twice before 'make install', it will remove the previous 'make' and you lose half of the work so separating single and double sources is required. Does it compile correctly using 12 cores? Using 8 or 16 on some of our machines the resulted binnaries were buggy and for that reason i added -j2 a long time ago before gromacs was first added to COMMUNITY (and never taken them away hehe) and kept -j'n' in makepkg.conf to build other packages that were not problematic. I agree with the merge, but MV is not the adequate solution to send GMXRC to profile.d and GMXRC is supposed to be a script which sources GMXRC.bash or else. I could patch GMXRC to install the correct script (to profile.d) instead of sourcing it and run it using a 'post install' directive (gromacs.install) or add GMXRC.csh and GMXRC.bash to profile.d as some packages do (firefox and xorg-server for instance).

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