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... 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.
