RE: [gmx-users] About parallel installation of GMX-4.5.1
Hi, Gromacs 4.5 compiles with a built-in thread mpi library by default. So you don't need --enable-mpi. With built in thread-mpi mdrun has an option -nt with by default uses all threads. Berk > From: lida...@gmail.com > Date: Sat, 11 Sep 2010 05:19:57 -0400 > Subject: Re: [gmx-users] About parallel installation of GMX-4.5.1 > To: gmx-users@gromacs.org > > I think you are right. > > 2010/9/11 wuxiao : > > Dear GMXers, > > I have a quad-core computer at hand, on which I would like to install a > > parallel implementation of GMX-4.5.1. The homepage > > (http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5) refers to > > "running on a multi-core node now uses thread-based parallelization to > > automatically spawn the optimum number of threads in the default build". I > > have a puzzle about it, that is, whether it means that I do not have to add > > "--enable-mpi" in compling the source for parallel calculations. Please give > > me some hints, thanks a lot. > > > > Chaofu Wu, Dr. > > > > -- > > 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 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/Support/Mailing_Lists > > > -- > 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 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/Support/Mailing_Lists -- 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 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/Support/Mailing_Lists
Re: [gmx-users] About parallel installation of GMX-4.5.1
I think you are right. 2010/9/11 wuxiao : > Dear GMXers, > I have a quad-core computer at hand, on which I would like to install a > parallel implementation of GMX-4.5.1. The homepage > (http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5) refers to > "running on a multi-core node now uses thread-based parallelization to > automatically spawn the optimum number of threads in the default build". I > have a puzzle about it, that is, whether it means that I do not have to add > "--enable-mpi" in compling the source for parallel calculations. Please give > me some hints, thanks a lot. > > Chaofu Wu, Dr. > > -- > gmx-users mailing list gmx-us...@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 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/Support/Mailing_Lists > -- 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 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/Support/Mailing_Lists
[gmx-users] About parallel installation of GMX-4.5.1
Dear GMXers, I have a quad-core computer at hand, on which I would like to install a parallel implementation of GMX-4.5.1. The homepage (http://www.gromacs.org/About_Gromacs/Release_Notes/Version_4.5) refers to "running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build". I have a puzzle about it, that is, whether it means that I do not have to add "--enable-mpi" in compling the source for parallel calculations. Please give me some hints, thanks a lot. Chaofu Wu, Dr. -- 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 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/Support/Mailing_Lists
Re: [gmx-users] g_hbond solvent insertion problem
Justin A. Lemkul skrev 2010-09-10 22.33: ceste...@unsl.edu.ar wrote: Hi all: I´m using gromacs version 4.0.2 and a box type truncated octahedron for the MD simulation. I need to analyze hydrogen bonds with solvent (water)insertion. I used the following command: g_hbond –f *.xtc –s *.tpr –n *.ndx –num num.xvg –dist *.xvg –ang *.xvg –a 45 –r 0.3 –ins. I selected acceptor and donor grups and solvent grup. The problem is that the file num.xvg is the same with direct hydrogen bonds (without solvent) and the output insert.dat is empty. Why is this? I don't think the -ins option has been functional for some time, and (I presume) it is for this reason that it was removed prior to the 4.5 release. -Justin Indeed. I am probably the one person who has spent most time developing g_hbond over the last two years or so and I'm not exactly sure of how the -ins option is supposed to work, why it doesn't work, and how it interferes with other g_hbond functionality. Don't expect it to be fixed soon, at least not by me. More likely, it will turn up as a separate tool when the analysis tools become more modular some time in the future. Erik Any help would be appreciated Carmen -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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 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/Support/Mailing_Lists
