[gmx-users] CECAM ScalaLife Workshop, Oct 03 - Oct 05, 2012

2012-06-08 Thread Rossen Apostolov
Dear GROMACS Users, GROMACS is one of the applications participating in the ScalaLife EU project (www.scalalife.eu). ScalaLife is organising a CECAM workshop on High Performance Computing in Computational Chemistry and Molecular Biology: Challenges and Solutions provided by ScalaLife

Re: [gmx-users] Question about the Gromacs website

2012-07-15 Thread Rossen Apostolov
Hi all, The root partition of the server was full. It should be working fine now. Cheers, Rossen On 7/15/12 8:03 PM, Justin Lemkul wrote: On 7/15/12 1:59 PM, Andrew DeYoung wrote: Hi, I have been not been able to access http://www.gromacs.org/ today. Has anyone else experienced this? I

[gmx-users] test, please ignore

2012-08-27 Thread Rossen Apostolov
test *test* /test/ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe

[gmx-users] Re: [gmx-developers] Mails rejected with The message's content type was not explicitly allowed

2012-08-27 Thread Rossen Apostolov
Hi, There was an issue with /multipart/ missing from the allowed mime types. Now HTML mails should be also accepted. Rossen On 7/5/12 3:24 PM, Rossen Apostolov wrote: Dear all, Recently the Gromacs mailing lists have been used for sending spam and viruses, and thus now only plain text

[gmx-users] Wednesday, 15 May: upgrading redmine.gromacs.org

2013-05-12 Thread Rossen Apostolov
Dear users and developers, On Wednesday the redmine server will be upgraded and moved to a new VM. Thus expect downtime of 1-2 hours (if it all goes well :-) ). Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] Re: [gmx-developers] Wednesday, 15 May: upgrading redmine.gromacs.org

2013-05-16 Thread Rossen Apostolov
Hi, The new server is up and running. Let us know if you see issues. Cheers, Rossen On 5/12/13 8:56 PM, Rossen Apostolov wrote: Dear users and developers, On Wednesday the redmine server will be upgraded and moved to a new VM. Thus expect downtime of 1-2 hours (if it all goes well

Re: AW: [gmx-users] Implicit Solvent

2010-01-21 Thread Rossen Apostolov
Hi Hans, On 01/21/2010 05:54 PM, Hans HEINDL wrote: Hola Deisy, I have used the implicit solvent which is built into mdrun-openmm. It works well: but there are some setbacks: 1. As far as I know it has only been tested with the amber 99 forcefield port for mdrun-openmm. (see

Re: [gmx-users] Problems with gromacs-openMM

2010-01-27 Thread Rossen Apostolov
Hi, try to do add the OpenMM library dir to your library path before running make $ export LD_LIBRARY_PATH=/opt/openmm/lib:$LD_LIBRARY_PATH Also, OpenMM support will be officially available in the next Gromacs release (soon). Rossen On 1/27/10 4:28 AM, jorge_quint...@ciencias.uis.edu.co

Re: [gmx-users] On the new web site, how does one make a user contribution?

2010-03-09 Thread Rossen Apostolov
Hi Бруце, Many users who registered on the old wiki were given a default status of viewers after the transition to the new site. I changed your status and now you should be able to edit pages across the site. Rossen On 03/09/2010 09:15 PM, Bruce D. Ray wrote: I went to the new web site to

Re: [gmx-users] OpenMM

2010-04-13 Thread Rossen Apostolov
Hi,O On 04/13/2010 04:23 PM, PACIELLO GIULIA wrote: Even if I have followed all the instructions reported for the correct installation of GPU, CUDA, OpenMM and even if my .mdp file for the simulation is written following the features supported in the release Gromacs-OpenMM, the output of the

[gmx-users] git server maintenance downtime

2011-05-09 Thread Rossen Apostolov
Hi, The git server may be temporarily offline today for maintenance. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please

[gmx-users] git server maintenance finished

2011-05-09 Thread Rossen Apostolov
Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take some time for the DNS to propagate. The old server is still available at git-old.gromacs.org, 130.237.25.210. We'll take it offline after we make sure the new one runs fine.

[gmx-users] Re: git server maintenance finished

2011-05-09 Thread Rossen Apostolov
The DNS seems to be finished updating now. Let me know if something doesn't work as expected with the new server. Cheers, Rossen On 5/9/11 5:25 PM, Rossen Apostolov wrote: Hi, The git server, git.gromacs.org, was moved to a new machine: tcbs03.theophys.kth.se, 130.237.25.132. It may take

Re: [gmx-users] Does current GROMACS-GPU support CMAP dihedrals in CHARMM

2011-05-16 Thread Rossen Apostolov
Hi, Only OpenMM-2.0 (no CMAP) is supported in the gromacs 4.5 releases. There are no plans at the moment to support all new functionality in OpenMM-3.0. Cheers, Rossen On 5/16/11 9:06 AM, Zhi Wang wrote: On 2011-5-14 0:52, zw...@cam.ac.uk wrote: Hello. I am writing to ask if current

Re: [gmx-users] Why does the -append option exist?

2011-06-04 Thread Rossen Apostolov
Hi, On Jun 4, 2011, at 19:11, Dimitar Pachov dpac...@brandeis.edu wrote: By the way, is this ever reviewed: Your mail to 'gmx-users' with the subject Re: [gmx-users] Why does the -append option exist? Is being held until the list moderator can review it for approval. This

Re: [gmx-users] gromacs 2.1

2011-06-13 Thread Rossen Apostolov
You can try also $ git tag release-1-6 release-1-6-01 release-2-0 release-2-0-01 release-2-0-02 release-3-0 release-3-1 release-3-1-1 release-3-1-2 release-3-1-3 release-3-1-4 release-3-2 v4.0.7 v4.5 v4.5-beta1 v4.5-beta2 v4.5-beta3 v4.5-beta4 v4.5.1 v4.5.2 v4.5.3 v4.5.4 # git checkout

[gmx-users] in preparation for 4.5.5 and 4.6 releases

2011-06-22 Thread Rossen Apostolov
Hi, We are preparing for a new maintenance release 4.5.5. It will fix critical open issues with previous releases, so please file your reports in redmine.gromacs.org by the end of June. After the 4.5.5 release, the stable branch will be frozen for bugfixes only, and new functionality will

Re: [gmx-users] Register

2011-07-06 Thread Rossen Apostolov
You can only register from the website: http://lists.gromacs.org/mailman/listinfo/gmx-users Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

[gmx-users] Fwd: inquiry

2011-07-18 Thread Rossen Apostolov
Please send your mails directly to the mailing list gmx-users@gromacs.org (cc:). Rossen Original Message Subject:inquiry Date: Sun, 17 Jul 2011 01:26:18 -0700 From: sara soleimanzadegan sara_soleimanzade...@yahoo.com Reply-To: sara soleimanzadegan

Re: [gmx-users] building GROMACS 4.5.4 on Power6 with CMAKE

2011-09-14 Thread Rossen Apostolov
Hi, On 9/13/11 4:27 PM, Mark Abraham wrote: On 14/09/2011 12:20 AM, Marcin Zielinski wrote: Ok, Using -DGMX_ACCELERATION=Power6 brings a plethora of new errors during the compilation. Firstly, including config.h inside the fortran .F kernel files for power6 is causing problems with their

[gmx-users] New maintenance release: 4.5.5

2011-09-21 Thread Rossen Apostolov
Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz. Some notable updates in this release: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending

[gmx-users] potential git server downtime

2010-07-28 Thread Rossen Apostolov
Hi, Due to construction work in the university building, the source code repository server git.gromacs.org may experience some downtime on Jul 29/30 (Thu/Fri). Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the

[gmx-users] GROMACS-4.5-beta1 is out!

2010-07-30 Thread Rossen Apostolov
After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is out! It is full of many new and exciting features, please try them out! If something is not working as expected, please send a mail or file a bugzilla report. For developers: there is a new branch for stable releases

Re: [gmx-users] GROMACS-4.5-beta1 is out!

2010-08-01 Thread Rossen Apostolov
On 07/31/2010 10:17 PM, ms wrote: As a young GROMACS user, thank you a lot! I just want to ask: On 30/07/10 20:20, Rossen Apostolov wrote: * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating

[gmx-users] new beta release - gromacs-4.5-beta2

2010-08-02 Thread Rossen Apostolov
Hi, Several important bugs in the previous beta have been fixed in this new release. Please try it out and let us know if it doesn't work as expected. We plan to have weekly beta releases so that the final stable 4.5 can be rolled out as soon as possible. So, the more bugs are found

Re: [gmx-users] What version of cmake is required to compile v4.5b2 for GPUs?

2010-08-03 Thread Rossen Apostolov
Hi Chris, Actually this was a mistake on the website, it must be CMake = 2.6.4, so 2.8.0 is fine. Although the build system requires CUDA 3.1, that doesn't seem to be the problem from your log. Did you get it to work? Rossen On 08/03/2010 01:06 AM, chris.ne...@utoronto.ca wrote: Ah, I

Re: [gmx-users] gmx 4.5 configure options confusing

2010-08-04 Thread Rossen Apostolov
Hi, This was a typo in configure.ac, the second line should say --without-qmmm-orca. Fixed it for the next release. Thanks for reporting. Rossen On 7/31/10 12:11 PM, Alan wrote: For gmx 4.5 beta, I see with ./configure --help: --without-qmmm-mopacUse modified Mopac 7 for QM-MM (see

Re: [gmx-users] tests for gmx 4.5

2010-08-04 Thread Rossen Apostolov
Hi, The tests haven't been ported to 4.5 yet but I hope to fix that before the final release. Rossen On 7/31/10 7:08 PM, Alan wrote: Is there a proper set of tests for gmx 4.5 because neither ftp://ftp.gromacs.org/pub/tests/gmxtest-4.0.4.tgz or git clone

Re: [gmx-users] compiling GPU 4.5b2, CUDA_INCLUDE_DIRECTORIES function is undefined

2010-08-06 Thread Rossen Apostolov
Hi Chris, ## what I did: module purge module load gcc/gcc-4.4.0 module load cmake/2.8.0 #need version =2.6.4 module load cuda/cuda-3.1 mkdir gpuexec export OPENMM_ROOT_DIR=/project/pomes/cneale/GPC/exe/OpenMM2.0-Source/exec/openmm cmake

[gmx-users] Test

2010-08-09 Thread Rossen Apostolov
-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to

Re: [gmx-users] tests for gmx 4.5

2010-08-09 Thread Rossen Apostolov
? Alternatively, we can just announce that the reference data was generated by the 3-3-version with a given git hash and not release. Thoughts? Mark - Original Message - From: Rossen Apostolov rossen.aposto...@cbr.su.se Date: Wednesday, August 4, 2010 17:56 Subject: Re: [gmx-users] tests for gmx 4.5

Re: [gmx-users] tests for gmx 4.5

2010-08-09 Thread Rossen Apostolov
- From: Rossen Apostolov rossen.aposto...@cbr.su.se Date: Wednesday, August 4, 2010 17:56 Subject: Re: [gmx-users] tests for gmx 4.5 To: gmx-users@gromacs.org Hi, The tests haven't been ported to 4.5 yet but I hope to fix that before the final release. Rossen On 7/31/10 7:08 PM, Alan

Re: [gmx-users] double precision pdb2gmx - 4.5beta2 - segmentation fault - icc compiler (gcc is fine)

2010-08-09 Thread Rossen Apostolov
This was already reported, there is a bugzilla filed already and we are looking at fixing it. http://bugzilla.gromacs.org/show_bug.cgi?id=495 Rossen On 8/6/10 2:45 PM, david.groc...@uk.fujitsu.com wrote: Has anyone else tried this ? The single precision version is fine with icc. Thanks

Re: [gmx-users] Gromacs-4 benchmarking

2010-08-10 Thread Rossen Apostolov
On 8/10/10 8:40 AM, vivek sharma wrote: Hi There, I want to benchmark the scalability and speed for gromacs-4 on our cluster. I want to know if there is any benchmarking activity already goin on? I have browsed and got benchmarking for gromacs-3 and it seems that gromacs-4 is much more

Re: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon Woodcrest

2010-08-10 Thread Rossen Apostolov
Hi, This bug is now fixed in git release-4-5-patches (commit 0a31a047f429). Rossen On 8/6/10 11:33 AM, david.groc...@uk.fujitsu.com wrote: Hi, this is the first time I have messaged this group, so please bear with me. I have had little trouble with previous versions (4.0.7 for example),

[gmx-users] New beta release: 4.5-beta3

2010-08-10 Thread Rossen Apostolov
New beta release of gromacs is available for testing: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5-beta3.tar.gz. Many bugs have been fixed in this release, mainly double precision support with icc compilers, SSE2. Have a look at the release note on the website for more details. There are

Re: [gmx-users] GMXRC missing

2010-08-10 Thread Rossen Apostolov
Hi Ondrej, I can confirm the problem. We'll fix it for the next release (unfortunately it didn't make it in -beta3). Rossen On 08/10/2010 04:13 PM, Ondrej Marsalek wrote: Dear all, I have installed 4.5 beta2 using cmake and it seems that the GMXRC files are missing in the installation.

Re: [gmx-users] GMXRC missing

2010-08-11 Thread Rossen Apostolov
Hi, I commited a patch in the latest git. Thanks for reporting, Rossen On 8/10/10 4:13 PM, Ondrej Marsalek wrote: Dear all, I have installed 4.5 beta2 using cmake and it seems that the GMXRC files are missing in the installation. Can anyone confirm this? Best, Ondrej -- gmx-users mailing

Re: [gmx-users] New beta release: 4.5-beta3

2010-08-11 Thread Rossen Apostolov
Hi, I can't compile using CMake - I get undefined references to GSL functions when compiling do_dssp. -lgsl seems to be missing from the linker line. GSL libraries support has been removed from the CMake system, you can use autoconf for now. The GSL and Gromacs licenses are not compatible

Re: [gmx-users] broken links

2010-08-11 Thread Rossen Apostolov
Hi Alan, Those links were pointing to the old wiki. I fixed them and now they refer directly to the original resources. Let us know if the page needs updating. Rossen On 08/11/2010 06:59 PM, Alan wrote: Hi there, I cannot download from

Re: [gmx-users] gromacs from git source and openmm failed

2010-08-12 Thread Rossen Apostolov
Hi, Try it again with the latest release-4-5-branch, Erik added a lot of fixes. Rossen On 8/12/10 1:11 PM, Alan wrote: Hi there, I am trying now to compile mdrun-openmm, by doing: cmake -DGMX_OPENMM=ON .. make mdrun -- Threads not compatible with OpenMM build, disabled CMake Warning at

Re: [gmx-users] Gromacs 4.5-beta2 forcefield troubles with the GPU version

2010-08-12 Thread Rossen Apostolov
Hi, I commited a fix and now all AmberFF are supported with the GPU version. The other forcefields are not supported at the moment. Rossen On 8/10/10 12:19 PM, Karel Berka wrote: Hi all, I am trying to get 4.5-beta2 running on graphic card but mdrun-gpu (gcc 4.1.3) is still complaining

Re: [gmx-users] Re: gromacs from git source and openmm failed

2010-08-12 Thread Rossen Apostolov
Hi, On 8/12/10 2:43 PM, Alan wrote: Thanks Rossen, Try it again with the latest release-4-5-branch, Erik added a lot of fixes. Indeed, when I did my report *was* with Erik's mods, which I am afraid, was what broke the compilation. I am using 'git log': Author: Rossen Apostolov ros

[gmx-users] gmx-developers mailing list search

2010-08-12 Thread Rossen Apostolov
Hi, I just updated the website and now you can search also the developers mailing list at http://www.gromacs.org/Support/Mailing_Lists/Search_gmx-developers_mailing_list . The quick link on the front page still takes you to the gmx-users list, so after that you have to click again in the

Re: [gmx-users] Re: dihedraltypes funct 4 and 9 in gmx 4.5 amber

2010-08-19 Thread Rossen Apostolov
On 8/19/10 8:51 AM, Berk Hess wrote: Hi, Yes, functiontype 1 and 4 are identical, except that the energy gets added to different terms in the log and energy file. In Gromacs 4.0 (and before) to get a dihedral potential consisting of a sum of cosines with different periodes you could do

[gmx-users] The last beta release: Gromacs-4.5-beta4

2010-08-27 Thread Rossen Apostolov
The last beta release of Gromacs-4.5-beta4 is available for download. The AMBER FF have been validated and are now production ready; the GPU code had a serious bug fixed, and there is a new tool g_pme_error (it will be incorporated in g_tune_pme soon though). Most of the critical issues

Re: [gmx-users] Problems with GPU-Version and implicit water models

2010-08-31 Thread Rossen Apostolov
Hi, On 08/31/2010 12:53 PM, Christian Mücksch wrote: Dear all, I am using Gromacs-4.5-beta4 and compiled the GPU-Version. So far only Amber-FF are working in the GPU-version. Gromacs-GPU supports only AMBER and CHARMM forcefields. By default, pdb2gmx enables the -cmap option, and cmap

[gmx-users] Gromacs-4.5 (final) is out!

2010-09-01 Thread Rossen Apostolov
It is finally here: *Gromacs-4.5* has been just released ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.tar.gz. All critical issues have been resolved to deliver a stable and powerful package full of many new features http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5. Big

[gmx-users] Please test the new Gromacs-4.5!

2010-09-02 Thread Rossen Apostolov
Dear users, Gromacs-4.5 is finally out and although all major and critical bugs have been cleared, we are aware that there are probably many small issues still left. We would like to ask all users to go ahead and *heavy* test run the code. For example, * compile on different

Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5

2010-09-02 Thread Rossen Apostolov
Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. A very short lived 4.5 (RIP) :) Rossen On 9/2/10 11:23 AM, Christian Mücksch wrote: Dear all, so I downloaded Gromacs-4.5 and

Re: [gmx-users] Problem with installing mdrun-gpu in Gromacs-4.5

2010-09-02 Thread Rossen Apostolov
On 9/2/10 11:46 AM, Carsten Kutzner wrote: On Sep 2, 2010, at 11:42 AM, Rossen Apostolov wrote: Hi, Yes, cmake is broken:) We forgot to add some of the cmake specific files for distribution (which is created using autoconf). I'll release a 4.5.1 right now. Hi Rossen, in ./src/tools

Re: [gmx-users] Please test the new Gromacs-4.5!

2010-09-02 Thread Rossen Apostolov
Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users. Rossen On 9/2/10 10:51 AM, Rossen Apostolov wrote: Dear users, Gromacs

Re: [gmx-users] Please test the new Gromacs-4.5!

2010-09-02 Thread Rossen Apostolov
SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 12:37 PM, Rossen Apostolov wrote: Hi, Some CMake specific files were missing from the distributed tarball and were breaking the build system. I've made a new release, 4.5.1, that has a working CMake support. Nothing has changed for autoconf users

Re: [gmx-users] Please test the new Gromacs-4.5!

2010-09-02 Thread Rossen Apostolov
Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re-download it again (I know it's not the right thing to do with releases though :-) ) Rossen Hi Rossen, thanks for this very helpful

Re: [gmx-users] Please test the new Gromacs-4.5!

2010-09-02 Thread Rossen Apostolov
On 9/2/10 3:21 PM, Florian Dommert wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 09/02/2010 02:56 PM, Rossen Apostolov wrote: Hi Florian, Thanks a lot! That was another miss. I have re-packaged 4.5.1 :) So if someone has downloaded it in the last couple of hours, please re

Re: [gmx-users] git gromacs

2010-09-07 Thread Rossen Apostolov
On 9/7/10 1:19 PM, Alan wrote: I am trying release-4-5-patches and now I can see it's compiling and installing. However, 'make install' puts the bins only in /usr/local/gromacs/bin and I don't have (or don't find) how to 'make links' or similar to have the gmx bins in /usr/local/bin. I am

Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

2010-09-13 Thread Rossen Apostolov
Hi Alan, There was a missing dependency for building gmx_gpu_utils, but for some reason compilation didn't break on linux:) This is now fixed in release-4-5-patches. Pay attention though that the prebuilt OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6 Rossen On 9/11/10

Re: [gmx-users] please help, cannot compile gmx 4.5 openmm

2010-09-13 Thread Rossen Apostolov
symbols: OpenMM::State::getVelocities() const, referenced from: snip . then you can force compilation for 32bit by: $ export CFLAGS='-arch i386' $ export CXXFLAGS='-arch i386' or recompile the openmm from source. Rossen On 9/13/10 1:01 PM, Rossen Apostolov wrote: Hi Alan

Re: [gmx-users] revive gmx-announce

2010-09-16 Thread Rossen Apostolov
Hi Inon, That's exactly what we talked about today at a developers' meeting. We'll be posting there announcements! Rossen On 2010-09-15 17.08, Inon Sharony wrote: Hi everyone! I saw that the recent proliferation of GROMACS 4.5 had a hiccup involved (hence 4.5.1), but I only caught this a

Re: [gmx-users] an example to test mdrun-gpu x mdrun

2010-09-18 Thread Rossen Apostolov
Hi Alan, On 9/14/10 3:21 PM, Alan wrote: Hi there, I am testing on a MBP 17 SL 10.6.4 64 bits and nvidia GeForce 9600M GT So I got mdrun-gpu compiled and apparently running, but when I try to run 'mdrun' to compare I have a segment fault. Any other comments to the md.mdp and em.mdp are

Re: [gmx-users] Simulations on GPU

2010-10-07 Thread Rossen Apostolov
Hi, On 10/6/10 3:48 AM, Igor Leontyev wrote: Szilárd wrote: The beta versions are all outdated, could you please use the latest source distribution (4.5.1) instead (or git from the release-4-5-patches branch)? The result is the same for both the distribution 4.5.1 and git from the

Re: [gmx-users] SwissParam

2010-10-07 Thread Rossen Apostolov
Thanks for contributing! I added a page about it on the Gromacs website: http://www.gromacs.org/Downloads/Related_Software/SwissParam Rossen On 10/7/10 7:13 PM, Michel Cuendet wrote: SwissParam, a web service that provides topologies and parameters for small organic molecules, compatible

[gmx-users] User training for Gromacs on parallel systems: a survey

2010-10-16 Thread Rossen Apostolov
Dear all, Gromacs is participating in the ScalaLife (http://scalalife.org/) European project aimed at improving the parallel performance of Life Science applications. An important part of the ScalaLife project is the dissemination of the results and user training. We have prepared a short

[gmx-users] New release: 4.5.2

2010-10-30 Thread Rossen Apostolov
Dear Gromacs users and developers, A new bugfix release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.2.tar.gz. Here is a list of some of the resolved issues for 4.5.1: * CHARMM force field now has single atom charge groups (pdb2gmx -nochargegrp no longer

Re: [gmx-users] Re: g_energy problem with 4.5.1 and 4.5.2

2010-11-02 Thread Rossen Apostolov
Hi, On 11/2/10 1:35 PM, Sander Pronk wrote: Hi Michael, I've just committed a fix to the git repository (it's in the release-4-5-patches branch) There were 2 problems - Energy files in double precision couldn't be read in 4.5.2, due to an overly strict error checking issue. - The box matrix

Re: [gmx-users] gpu

2010-11-07 Thread Rossen Apostolov
Hi, Did you read this? http://www.gromacs.org/gpu Rossen On 11/7/10 1:23 PM, Erik Wensink wrote: Dear gmx-users, How to invoke the gpu for simulations, e.g. is there (compiler) flag? Cheers, Erik -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] New release: 4.5.2

2010-11-09 Thread Rossen Apostolov
Dear Gromacs users and developers, A new maintenance release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz. It fixes: * Double precision energy file reading * CHARMM and GB issues * Support for Altivec (PowerPC) with CMake * Running binaries within the

[gmx-users] Re: [gmx-developers] New release: 4.5.3

2010-11-09 Thread Rossen Apostolov
Ooops! Made a mistake in the subject, it was supposed to be 4.5.3 :) Rossen On 11/9/10 10:39 PM, Rossen Apostolov wrote: Dear Gromacs users and developers, A new maintenance release of Gromacs is now available: ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.3.tar.gz. It fixes: * Double

[gmx-users] Mailing List Search on the new website

2009-09-29 Thread Rossen Apostolov
Hi, It is now possible to search the mailing list archives from the new website: http://www.gromacs.org/Support/Mailing_Lists/Search . There is a link to it at the Quick Links section on the front page also. Currently: * Only the [gmx-users] mailng list is being indexed. * The index is

Re: [gmx-users] Mailing List Search on the new website

2009-09-30 Thread Rossen Apostolov
Hi Mark and David, I agree with the points you make. The change was rather abrupt but in the long term I believe the dekiwiki will be a much better and useful platform. The dekiwiki has been initially developed on top of mediawiki with the aim to make it more user friendly to modify

Re: [gmx-users] mailing list search

2009-10-07 Thread Rossen Apostolov
Hi, I made some updates and incorrectly changed the permissions. You should be able to search now even without logging in. Rossen Sun Joo Lee wrote: Hello I have been trying to search the mailing list after I logged in to the new gromacs website. But I do not get any searched results but

Re: [gmx-users] mailing list search

2009-10-08 Thread Rossen Apostolov
Hi, I registered yesterday and I am logged in, but perhaps I am not registered as contributor... I added you as a contributor. Thanks for offering to help! New users are only viewers by default to avoid giving instant write permissions to everyone. People who would like to

Re: [gmx-users] mailing list search

2009-10-13 Thread Rossen Apostolov
Update: I set a limit of 500 results from any query. The server shouldn't hang anymore. Rossen Apostolov wrote: Hi, You don't need to register or login if you want to search the mailing list. All searches for words of 3 letters or less, for example pdb, are ignored and you'll get a blank

Re: [gmx-users] searching mailing lists other than gmx-users

2009-11-01 Thread Rossen Apostolov
at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Rossen Apostolov Center for Biomembrane Research Department

Re: [gmx-users] Problem regarding Gromacs - GPU

2010-11-23 Thread Rossen Apostolov
Hi, The benchmarks are infinite runs (nsteps=-1). Try adding the -maxh option to mdrun to limit the execution time. Rossen On 11/23/10 9:48 AM, kapil mathur wrote: Dear All, I have some queries regarding the benchmarking result of mdrun-gpu : 1. I have run mdrun-gpu with

Re: [gmx-users] 3 questions of gromacs 4.5.2 for both CPU and GPU

2010-11-24 Thread Rossen Apostolov
Hi, On 11/24/10 2:59 AM, lin hen wrote: hi, I am testing the dhfr benchmarks with gromacs 4.5.2 1. for the benchmarks: dhfr-solv-RF-1nm.bench and dhfr-solv-RF-2nm.bench, set the steps = 1, The GPU version running results shows as following: ./mdrun-gpu Pre-simulation ~15s

Re: [gmx-users] compilation instructions, the gromacs wiki, documentation, and test suites

2010-12-22 Thread Rossen Apostolov
Hi, On 12/22/10 4:39 AM, Justin A. Lemkul wrote: chris.ne...@utoronto.ca wrote: Dear Roland: I am not sure what my barrier is electronically, only that there is a barrier. The web site has changed since my last attempt to make modifications, but I still can not add to the site as I once

Re: [gmx-users] Simulations on GPU

2011-01-04 Thread Rossen Apostolov
On 1/4/11 3:16 PM, Francesco Oteri wrote: Maybe the used force-field is wrong. mdrun-gpu is able to use the AMBER forcefield, but it is not possible using gromos force-field. When gromos force-field is used, the output is full of NaN Is that the case? mdrun should complain and exit if the FF

Re: [gmx-users] Simulations on GPU

2011-01-14 Thread Rossen Apostolov
Hi, I get this error when I try to run mdrun-gpu with a forcefield that has GROMOS interaction types: Fatal error: OpenMM does not support (some) of the provided interaction type(s) (G96Angle). Maybe it's possible to run a short simulation on a small system and not encounter the missing

[gmx-users] www site is temporarily down

2011-03-02 Thread Rossen Apostolov
Hi all, There was a power outage which affected the www.gromacs.org server. The system is being fixed at the moment and therefore unreachable. We expect it to be online soon though. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] New maintenance release: gromacs-4.5.4

2011-03-21 Thread Rossen Apostolov
Dear Gromacs community, A new maintenance release of Gromacs is available for download at ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.4.tar.gz. Some notable updates in this release: * Fixed pdb2gmx picking up force field from local instead of library directory * Made pdb2gmx vsite

[gmx-users] New version 4.5.4 of the Gromacs manual

2011-03-22 Thread Rossen Apostolov
Dear all, The updated version 4.5.4 of the Gromacs manual is available at ftp://ftp.gromacs.org/pub/manual/manual-4.5.4.pdf. Happy simulating! Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at

Re: [gmx-users] Various web issues

2011-03-22 Thread Rossen Apostolov
Hi Justin, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: Hi, I posted this a few days ago, but the problem persists - the search feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very

Re: [gmx-users] Various web issues

2011-03-22 Thread Rossen Apostolov
Hi again, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: I posted this a few days ago, but the problem persists - the search feature on the Gromacs site either returns an error or completely nonsensical content. Can someone please look into why this is so? Manual navigation is very tedious.

Re: [gmx-users] Various web issues

2011-03-23 Thread Rossen Apostolov
Hi Justin, On 3/22/11 6:57 PM, Justin A. Lemkul wrote: 1. manual.gromacs.org no longer has any useful content. The site comes up with syrah.cbr.su.se and nothing else. Are there changes going on with this site? I moved the manual to the new server and now it's accessible again. Cheers,

Re: [gmx-users] Web site issues (Search, Redmine)

2011-03-31 Thread Rossen Apostolov
Hi Lutz, On 3/31/11 9:06 PM, Lutz Maibaum wrote: I ran into some issues with the Gromacs web site: 1. I tried to register an account on the bug tracker (http://redmine.gromacs.org/account/register). Upon entering my information, I get the odd error message Email notifications is not included

[gmx-users] If your mails are rejected from the list

2013-05-23 Thread Rossen Apostolov
Hi everyone, Many users ask why their mails are being automatically rejected from posting. Almost always it's due to one of two reasons: * *The messages are too big*. - Messages*larger than 50KB* are *rejected*. Please include large attachments as *links **for download* from an external ftp

[gmx-users] mailing list migration

2013-11-14 Thread Rossen Apostolov
Hi, Today we are migrating the mailinglist server to a new machine, so there might be delays in the delivery of messages. Cheers, Rossen -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at