[gmx-users] Selecting certain types of atoms from trajectory file with C++ code
Dear users, Recently I have been trying to use "xdrfile" libray to read trajectory ".trr" file in my own C++ code. Now I can just read the coordinates of all atoms at each time frame. But I don't know how to select certain types of atoms from the trajectory file. Although the graomcs tool "make_ndx" can do this, but i need to do it with C++ codes for the purpose of further analysis. Does someone have any experience about this? Your reply would be greatly appreciated. Thanks, Zhikun -- 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] gmx 4.6 mpi installation through openmpi?
Sorry, Hrachya Astsatryan, I have no idea in such case. Why not just try to install openmpi and fftw ahead by yourself before installing groamcs? On Mon, Apr 8, 2013 at 4:06 PM, Hrachya Astsatryan wrote: > Dear Zhikun Cai, > > Thank you for your quick response. > > > On 4/8/13 11:15 AM, Zhikun Cai wrote: > > Hi, see installation instruction with CMAKE here: > > > > http://www.gromacs.org/Documentation/Installation_Instructions > > > > I guess that maybe you need to specify your Openmpi and FFTW installation > > directories using options CMAKE_PREFIX_PATH. > > For example, my Openmpi and FFTW were firstly installed in > > "/home/ucaizk/ComTools/openmpi" and "/home/ucaizk/ComTools/fftw > > Then, I installed gromacs with command lines below: > wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.1.tar.gz > > $ tar -xzvf gromacs-4.6.1.tar.gz > > $ mkdir build > > $ cd build > Done > > $ > > > CMAKE_PREFIX_PATH=/home/ucaizk/ComTools/openmpi:/home/ucaizk/ComTools/fftw > export CMAKE_PREFIX_PATH=/opt/mpi (I use an option below to download and > install the fftw by gromacs) > > cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX > > =/home/ucaizk/ComTools/gromacs ../gromacs-4.6.1 > cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/backup/sicnas/gromacs > -DGMX_BUILD_OWN_FFTW=ON (I want to install on /backup/sicnas/gromacs, > which is shared by nodes) > > $ make > > $ make install > done! > > And finally get the following error: > /backup/sicnas/gromacs/bin/mdrun_mpi: error while loading shared > libraries: libblas.so.3: cannot open shared object file: No such file or > directory > > > When above was done, cd to your home directory and add one line to > > ".bashrc" file > > export PATH=$PATH:/home/ucaizk/ComTools/gromacs/bin > > > > restart bash shell, then all are done! > > > > Hope it helps! > > > > Zhikun > > > > > > On Fri, Apr 5, 2013 at 11:12 PM, 라지브간디 wrote: > > > >> Dear gmx users, > >> > >> > >> I could able to install gmx4.6.1 without MPI option in my cluster, > whereas > >> the MPI fails to install and gives the following error ( used command > line > >> cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON ) > >> > >> > >> CMake Error at cmake/gmxManageMPI.cmake:161 (message): > >> MPI support requested, but no MPI compiler found. Either set the > >> C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called > mpicc), > >> or > >> set the variables reported missing for MPI_C above. > >> Call Stack (most recent call first): > >> CMakeLists.txt:494 (include) > >> > >> > >> > >> > >> I have also installed openmpi 1.5 version. which mpirun shows > >> /usr/bin/mpirun. > >> It seems openmpi installed in /usr/bin/openmpi/ > >> > >> > >> I dont know how to do link this cmake. > >> > >> > >> Please need some suggestion. Thanks. > >> > >> -- > >> 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 > >> > > > -- > Hrachya Astsatryan > Head of HPC Laboratory, > Institute for Informatics and Automation Problems, > National Academy of Sciences of the Republic of Armenia > 1, P. Sevak str., Yerevan 0014, Armenia > t: 374 10 284780 > f: 374 10 285812 > e: hr...@sci.am > skype: tighra > -- > 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] gmx 4.6 mpi installation through openmpi?
Hi, see installation instruction with CMAKE here: http://www.gromacs.org/Documentation/Installation_Instructions I guess that maybe you need to specify your Openmpi and FFTW installation directories using options CMAKE_PREFIX_PATH. For example, my Openmpi and FFTW were firstly installed in "/home/ucaizk/ComTools/openmpi" and "/home/ucaizk/ComTools/fftw Then, I installed gromacs with command lines below: $ tar -xzvf gromacs-4.6.1.tar.gz $ mkdir build $ cd build $ CMAKE_PREFIX_PATH=/home/ucaizk/ComTools/openmpi:/home/ucaizk/ComTools/fftw cmake -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX =/home/ucaizk/ComTools/gromacs ../gromacs-4.6.1 $ make $ make install When above was done, cd to your home directory and add one line to ".bashrc" file export PATH=$PATH:/home/ucaizk/ComTools/gromacs/bin restart bash shell, then all are done! Hope it helps! Zhikun On Fri, Apr 5, 2013 at 11:12 PM, 라지브간디 wrote: > Dear gmx users, > > > I could able to install gmx4.6.1 without MPI option in my cluster, whereas > the MPI fails to install and gives the following error ( used command line > cmake .. -DGMX_MPI=ON -DGMX_BUILD_OWN_FFTW=ON ) > > > CMake Error at cmake/gmxManageMPI.cmake:161 (message): > MPI support requested, but no MPI compiler found. Either set the > C-compiler (CMAKE_C_COMPILER) to the MPI compiler (often called mpicc), > or > set the variables reported missing for MPI_C above. > Call Stack (most recent call first): > CMakeLists.txt:494 (include) > > > > > I have also installed openmpi 1.5 version. which mpirun shows > /usr/bin/mpirun. > It seems openmpi installed in /usr/bin/openmpi/ > > > I dont know how to do link this cmake. > > > Please need some suggestion. Thanks. > > -- > 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] Inhomogeneity of water molecules insertion into the box
Hi all, I would like to add 484 water molecules into the box using command: genbox -cp newbox.gro -cs tip4p.gro -maxsol 484 -p topol.top -o solvated.gro What I expected is those water molecules would be randomly inserted into the box and the box should appear homogeneous. But the result disappointed me. Throught VMD, I found that the 484 water molecues was inserted almost in one half of the box. Then when I added more water molecules, they began to occupy the other half box. So what could I do to make the inserted 484 water molecules randomly positioned in the box in the beginning? Your advice would be highly appreciated. Zhikun -- 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] How to have two proteins randomly positioned and oriented in the box
Thank you, Justin. Your online tutorial helped me a newbie a lot. I ever tried using genbox -ci -nmol to insert two proteins in a specific box. But it didn't work. Nothing was inserted into the box. Maybe enlarging the box would work. I would try. On Mon, Apr 1, 2013 at 10:21 AM, Justin Lemkul wrote: > > > On 3/31/13 9:51 PM, Zhikun Cai wrote: > >> Hi everyone, >> >> I am trying to insert two same proteins in a simulation box. Now I have >> used pdb2gmx to convert one protein's pdb file to gro file. Then how >> should >> I do? How could they be randomly positioned and oriented in the box? >> > > Place them however you like within the box using editconf -center, > -translate, -rotate, etc as necessary. You may be able to get completely > random insertion with genbox -ci -nmol, but I've never tried it with a > protein. > > -Justin > > -- > ==**== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==**== > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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] How to have two proteins randomly positioned and oriented in the box
Hi everyone, I am trying to insert two same proteins in a simulation box. Now I have used pdb2gmx to convert one protein's pdb file to gro file. Then how should I do? How could they be randomly positioned and oriented in the box? Thanks in advance. Zhikun -- 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
