On Sun, Mar 28, 2021 at 21:11 Satyen Dhamankar <[email protected]> wrote:
> Hi Christoph, > > Thank you for your advice. I used spack to obtain all of my dependencies > using the script: > git clone clone https://github.com/spack/spack.git spack > source spack/share/spack/setup-env.sh > spack install votca-csg > > I am going through your tutorials, but I am trying to find the directory > where all the executables are so I can run the commands csg_map, csg_dump > and so on. At the moment, I am trying to execute the csg_stat and csg_map > command (in the atomistic spce simulation), but bash is not finding those > commands... > You can use “spack find -p votca-csg” to see the path. Also see https://spack.readthedocs.io/en/latest/basic_usage.html#using-installed-packages on how to use installed spack packages. Christoph > > I really appreciate all of your help! > On Thursday, March 25, 2021 at 11:07:43 PM UTC-4 Christoph Junghans wrote: > >> On Thu, Mar 25, 2021 at 20:52 Satyen Dhamankar <[email protected]> wrote: >> >>> Thank you so much for your response Christoph! >>> >>> when I do gmx -h on my cluster, I still see the following piece in my >>> output: >>> >>> GROMACS: gmx, version 2020.5 >>> >>> Executable: /home/satyend/.local/bin/gmx >>> >>> Data prefix: /home/satyend/.local >>> >>> Working dir: /home/satyend >>> >>> Command line: >>> gmx -h >>> >>> Does this mean that there is something wrong with my installation of >>> votca? Should I get a fresh copy of Gromacs which is less than 2020.5 (19.6 >>> perhaps)? >>> >> If you aren’t planning to use gromacs don’t worry about it, otherwise you >> will need an older version. Gromacs 2019.* is the last series that supports >> tabulated potentials. >> >> >>> I will get on with updating my gcc version and obtaining Eigen. >>> >> Alternatively try to use spack to install VOTCA. >> See >> https://www.votca.org/INSTALL.html#spack >> >> Christoph >> >>> >>> Again, I really appreciate you taking the time to answer my questions! >>> On Thursday, March 25, 2021 at 10:32:05 PM UTC-4 Christoph Junghans >>> wrote: >>> >>>> On Thu, Mar 25, 2021 at 8:20 PM Satyen Dhamankar <[email protected]> >>>> wrote: >>>> > >>>> > Hello, >>>> > >>>> > I am new to coarse-graining and VOTCA, and I want to install VOTCA to >>>> run coarse-grained simulation in GROMACS. I use GROMACS 2020.5, and have it >>>> on my system. >>>> Gromacs 2020.5 won't work as it doesn't have support for tabulated >>>> interactions. You build VOTCA with BUILD_OWN_GROMACS=ON below, so it >>>> will download and build gromacs 2019.6 for you. >>>> > >>>> > I used the following script to get votca on to my system, built for >>>> GROMACS, obtained from https://www.votca.org/csg-tutorials/README.html >>>> > >>>> > prefix=~/votca >>>> > >>>> > version=master # or 'stable' or 'v1.4.1' >>>> > >>>> > git clone -b ${version} --recursive >>>> https://github.com/votca/votca.git >>>> > >>>> > cd votca >>>> > >>>> > mkdir build >>>> > >>>> > cd build >>>> > >>>> > cmake -DBUILD_OWN_GROMACS=ON .. >>>> > >>>> > make -j5 >>>> > >>>> > make install >>>> > >>>> > I collected the stderr and stdout after running this script and >>>> attached it to this file. >>>> Looking at your output, it seems eigen is missing. CMake warns about >>>> that a couple of times. Also you gcc might be a bit old. >>>> >>>> > >>>> > My question is, is the software package that I have downloaded meant >>>> for GROMACS simulations, and GROMACS simulations only? Would I need to >>>> download the non-GROMACS version if I were running simulation using LAMMPS? >>>> VOTCA will support all MD packages that are on the system. Only >>>> gromacs needs to be there at compile time, the others just need to be >>>> there at runtime. >>>> If you are planning to use LAMMPS you can also build VOTCA without >>>> gromacs support. >>>> >>>> > >>>> > Should I be concerned by the standard output/standard errors that >>>> have taken place? there seem to be plenty of things, and I honestly don't >>>> know how to process all of the information... >>>> Yes, see my comments above. >>>> >>>> Christoph >>>> >>>> > >>>> > Thank you for any advice you have! >>>> > >>>> > Satyen >>>> > >>>> > -- >>>> > Join us on Slack: https://join.slack.com/t/votca/signup >>>> > --- >>>> > You received this message because you are subscribed to the Google >>>> Groups "votca" group. >>>> >>> > To unsubscribe from this group and stop receiving emails from it, send >>>> an email to [email protected]. >>>> > To view this discussion on the web visit >>>> https://groups.google.com/d/msgid/votca/c7de45e4-68de-4f46-ad08-8da9a28377c6n%40googlegroups.com. >>>> >>>> >>>> >>>> >>>> -- >>>> Christoph Junghans >>>> Web: http://www.compphys.de >>>> >>> -- >>> Join us on Slack: https://join.slack.com/t/votca/signup >>> --- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected]. >>> >> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/92d7824b-6f71-4af5-8f6c-be194b832ddcn%40googlegroups.com >>> <https://groups.google.com/d/msgid/votca/92d7824b-6f71-4af5-8f6c-be194b832ddcn%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/5c01873c-29d1-4f10-ac61-c44aafd55719n%40googlegroups.com > <https://groups.google.com/d/msgid/votca/5c01873c-29d1-4f10-ac61-c44aafd55719n%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e52JK2eQwQswqF%2BN5eEC-9bJDL70iX3BVa9Lro6i8zmnw%40mail.gmail.com.
