Re: [gmx-users] Concatenate .edr file
Qi Yan wrote: > Does anybody really know how to concatenate .edr file, since "trjcat" > concatenates only trajectory files. Manual section 7.4 Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with runtype start
Mark, I just checked and it seems I was consulting a manual for an older version than 3.3.1! I guess it was taken out in 3.3.1 Sorry for not being more careful. Thank you. -Dina On 10/20/07 4:16 PM, "Mark Abraham" <[EMAIL PROTECTED]> wrote: > dtmirij wrote: >> I searched the on line document for runtype and got nothing. But in the >> Manual in chapter 6 there is an overveiw of the pull code options and one of >> the options listed is the "starting structures" and it says the keyword for >> runtype to use for this is "start". > > http://www.gromacs.org/content/view/27/42/ > > Neither "starting structures" nor "start" (in this context) are > mentioned in the 3.3.1 manual?? > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with runtype start
dtmirij wrote: I searched the on line document for runtype and got nothing. But in the Manual in chapter 6 there is an overveiw of the pull code options and one of the options listed is the "starting structures" and it says the keyword for runtype to use for this is "start". http://www.gromacs.org/content/view/27/42/ Neither "starting structures" nor "start" (in this context) are mentioned in the 3.3.1 manual?? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Concatenate .edr file
Use eneconv program Marcelo On 10/20/07, Qi Yan <[EMAIL PROTECTED]> wrote: > > Does anybody really know how to concatenate .edr file, since "trjcat" > concatenates only trajectory files. > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Lic. Marcelo F. Masman Department of Molecular Neurobiology, Faculty of Mathematics and Natural Sciences, University of Groningen. Kerklaan 30 9751 NN Haren, Groningen The Netherlands Tel. +31 50 363 2299 Fax. +31 50 363 2331 email: [EMAIL PROTECTED] o Universidad Nacional de San Luis Facultad de Química, Bioquímica y Farmacia Departamento de Química Área de Química General e Inorgánica Cátedra de Química General TEL: +54-02652-424689 Interno: 158 Chacabuco 917. San Luis -(5700)- Argentina. o ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Concatenate .edr file
Does anybody really know how to concatenate .edr file, since "trjcat" concatenates only trajectory files. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pull code with runtype start
I searched the on line document for runtype and got nothing. But in the Manual in chapter 6 there is an overveiw of the pull code options and one of the options listed is the "starting structures" and it says the keyword for runtype to use for this is "start". On 10/19/07 6:55 PM, "Mark Abraham" <[EMAIL PROTECTED]> wrote: > dtmirij wrote: >> Hello everyone, >> >> I just want to clarify if the runtype "start" option works in gromacs-3.3.1. >> I didn't see anything in the mailings list suggesting that it doesn't. > > Did you try searching the manual for "runtype"? > > Mark > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Postdoc position available (virtual reality, interactive simulations)
Hi, following Erik Lindahl's suggestion to send more postdoc offers to this list, I couldn't resist. Although it is not clearly stated, the position below will also include some work on MD, and Gromacs in particular, so I thought it might be relevant to this list and audience. Cheers, Marc Baaden Virtual Reality in Computational Biology - Postdoctoral position at IBPC, Paris, France Postdoc position FlowVR Nano: a virtual laboratory Project description (see also http://www.shaman.ibpc.fr/fvnano_postdoc.pdf) We are seeking a highly motivated research programmer or a postdoctoral fellow to develop software tools for interactive high performance simulations coupling virtual reality, scientific visualization and parallel simulation through a full cooperation with on-going projects. The main application at the centre of this project targets handling and exploring simulations of biological or physical complex objects at the nanoscopic scale, using a virtual reality platform with haptic feedback. The successful candidate will join our group developing state-of-the-art computer simulation methods. This position is a unique training opportunity in a multi-disciplinary environment in collaboration with three other leading teams in France who are experts on complementary topics. Qualification and experience The candidate should have a PhD in visualisation, computer graphics, virtual reality or a related field. Skills in haptics would be appreciated. Specific experience with scientific computing in general and computational biology in particular is not required, but would represent an important advantage over other candidates. Strong skill in computer programming (in particular Objective-C, Cocoa), VTK or virtual reality and a good background in computer science is also an important prerequisite. Ability to work effectively in a team-based environment and leadership qualities are essential. Funding is available immediately. About the host institute The "Institut de Biologie Physico-Chimique" was created in 1930 by the Foundation Edmond de Rothschild. It is associated with the CNRS (Centre National de la Recherche Scientifique), a leading international scientific institution offering an exceptional environment to scientists early in their career. Closing date: 20 November 2007 Interested candidates should send a CV and a letter of motivation as PDF document to [EMAIL PROTECTED] Please include the names of three referees. When? 3 years starting Jan 2008 Where? Laboratoire de Biochimie Theorique, Paris, France Salary: 2500 Euro/month Project Leader: Marc Baaden Website: http://www.baaden.ibpc.fr/projects/fvnano -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:[EMAIL PROTECTED] - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] 1 out of 14 complex tests FAILED in GROMACS 3.3.1 installation dec+water
himanshu khandelia wrote: Hi, I used the test set for 3.3.2 on my 3.3.1 installation, and only one of the 14 tests failed. The log files and .out files from the pertinent failed test are attached. I am guessing that this test would run well only on 3.3.2 ? please read the wiki page on the test set. these are most likely negligible differences. Thank you very much for the help, -Himanshu ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
