On Wed, Jul 21, 2021 at 3:15 PM Mohsen Farshad <[email protected]> wrote: > > Thank you very much! I have still a single remaining confusion. > > Does this mean if I use atomistic configuration and topology files with GC > potential table, the system automatically runs coarse-grained simulation > using the following commands:
No you will have to use a cg topology and configuration file. For the former you can csg_ gmxtopol, which will generate a good starting point. For the latter, you can just map the atomistic configuration file. Christoph > > gmx grompp -f grompp.mdp - p topol.top -c conf.gro > gmx mdrun -table table_CG_CG.xvg > > where conf.gro and topol are atomistic configuration and topology files, and > table_CG_CG.xvg is the potential table extracted from FM technique. > > Thanks, > Mohsen > > > > On Wed, Jul 21, 2021 at 5:09 PM Christoph Junghans <[email protected]> wrote: >> >> On Wed, Jul 21, 2021 at 12:45 PM Mohsen Farshad >> <[email protected]> wrote: >> > >> > Hi Christoph, >> > >> > Is this correction answer to my question number 2, "Does the FM technique >> > aim to extract a table potential for CG system from the atomistic system >> > with matching the forces? Can we use this extracted FM potential table for >> > CG simulations --- not IBI, just normal CG MD simulation? If so would you >> > please let me know how can I use this potential table to run CG >> > simulations and what files are needed for that?": >> > >> > gmx grompp -f grompp.mdp - p topol.top -c confout.gro >> > gmx mdrun -table table_CG_CG.xvg >> > >> > where confout.gro is GC configuration file, and table_CG_CG.xvg is the >> > potential table extracted from FM technique. >> Yes that that is correct, but can also use the mapped atomistic >> conf.gro instead of confout.gro >> >> Christoph >> > >> > Thanks, >> > Mohsen >> > >> > On Wed, Jul 21, 2021 at 11:56 AM Mohsen Farshad <[email protected]> >> > wrote: >> >> >> >> Thanks for the explanation. I have still some difficulty understanding >> >> the process, and I have the following questions: >> >> >> >> 1. Are C6 and C12 are literally summed up ("+") or they are just combined >> >> during the FM process --- essentially they have not ever gotten separated? >> >> >> >> 2. Does the FM technique aim to extract a table potential for CG system >> >> from the atomistic system with matching the forces? Can we use this >> >> extracted FM potential table for CG simulations --- not IBI, just normal >> >> CG MD simulation? If so would you please let me know how can I use this >> >> potential table to run CG simulations and what files are needed for that? >> >> >> >> Thank you, >> >> Mohsen >> >> >> >> On Tue, Jul 20, 2021 at 5:07 PM Christoph Junghans <[email protected]> >> >> wrote: >> >>> >> >>> On Tue, Jul 20, 2021 at 8:47 AM Mohsen Farshad >> >>> <[email protected]> wrote: >> >>> > >> >>> > Thanks for the explanation. I am a bit confused. Is there any >> >>> > repulsion term in the Votca potential? Would you please explain what >> >>> > kind of potential is that? >> >>> >> >>> Gromacs just has the C6 and C12 tables columns, but in the case of >> >>> VOTCA we just add the C6 and C12 parts together and you can make one >> >>> of them zero. >> >>> (see >> >>> https://manual.gromacs.org/documentation/2019.5/reference-manual/special/tabulated-interaction-functions.html#user-specified-potential-functions) >> >>> Basically because it is not easy to separate the C6 from the C12 part >> >>> and also because you can do some funky things by using the C6 part for >> >>> something else. >> >>> >> >>> > >> >>> > Also in SPCE tutorial, to run CG simulation, it is suggested to use >> >>> > the files for ibi example. I have a few questions in regards to this >> >>> > part of the tutorial: >> >>> > >> >>> > 1. What command should I use to run coarse grain: >> >>> > >> >>> > "gmx grompp" and then "gmx mdrun -v" >> >>> This runs a MD simulation directly only use that after coarse-graining >> >>> or for atomistic simulation. >> >>> >> >>> > >> >>> > or "csg_inverse --options settings.xml" >> >>> This is the right command to do IBI >> >>> >> >>> > >> >>> > 1. Would you explicitly explain how should I adjust the settings.xml >> >>> > to make it compatible with the potential table that comes from FM. The >> >>> > current IBI setting.xml uses IBI interactive algorithm. Is that needed >> >>> > to run CG simulation using FM potential? --- if setting.xml is not >> >>> > needed please ignore this question. >> >>> >> >>> FM is a different CG method than IBI. FM is one shot and done, while >> >>> IBI is iterative. >> >>> You could use the FM potential as a starting potential for IBI, but >> >>> this is kind of pointless as FM matches the forces, while IBI matches >> >>> the structure. >> >>> >> >>> > >> >>> > 3. For CG simulation the CG configuration should be used or atomistic >> >>> > one? >> >>> The CG one. >> >>> >> >>> Christoph >> >>> >> >>> > >> >>> > Thank you, >> >>> > Mohsen >> >>> > >> >>> > >> >>> > On Mon, Jul 19, 2021 at 10:38 PM Christoph Junghans >> >>> > <[email protected]> wrote: >> >>> >> >> >>> >> On Mon, Jul 19, 2021 at 5:47 PM Mohsen Farshad >> >>> >> <[email protected]> wrote: >> >>> >> > >> >>> >> > Here are the potential, force, and output potentials. Would you >> >>> >> > please let me know whether they are correct? >> >>> >> The outcomes are actually correct. >> >>> >> >> >>> >> Your forces and the potential ends at 0.9nm and so is the xvg file. >> >>> >> The values smaller than 0.9nm are not zero. >> >>> >> We shift the potential in such a way that it is zero at the cutoff, >> >>> >> hence all values for r> 0.9nm are zero. >> >>> >> We put the values in the C12 column of the gromacs xvg table, hence >> >>> >> columns 2-5 are empty and only columns 6+7 have numbers. >> >>> >> >> >>> >> Christoph >> >>> >> > >> >>> >> > Thank you, >> >>> >> > Mohsen >> >>> >> > >> >>> >> > On Mon, Jul 19, 2021 at 6:34 PM Christoph Junghans >> >>> >> > <[email protected]> wrote: >> >>> >> >> >> >>> >> >> On Mon, Jul 19, 2021 at 3:04 PM Mohsen Farshad >> >>> >> >> <[email protected]> wrote: >> >>> >> >> > >> >>> >> >> > Hi Christoph, >> >>> >> >> > >> >>> >> >> > I was able to install the Votca using Spack. However, going >> >>> >> >> > through the tutorial I confronted an error after executing the >> >>> >> >> > following command: >> >>> >> >> > >> >>> >> >> > csg_call table integrate CG-CG.force CG-CG.pot >> >>> >> >> > >> >>> >> >> > The last lines of the error is as follows: >> >>> >> >> > >> >>> >> >> > #000: >> >>> >> >> > /tmp/tuo98996/spack-stage/spack-stage-hdf5-1.10.7-3mcrng3jtezm72xs2i2fbwpwzogxsupf/spack-src/src/H5T.c >> >>> >> >> > line 1708 in H5Tcopy(): not a datatype or dataset >> >>> >> >> > >> >>> >> >> > major: Invalid arguments to routine >> >>> >> >> > >> >>> >> >> > minor: Inappropriate type >> >>> >> >> > >> >>> >> >> > Running subscript 'table_integrate.pl CG-CG.force CG-CG.pot' >> >>> >> >> > (from tags table integrate) dir >> >>> >> >> > /home/tuo98996/spack/opt/spack/linux-centos7-broadwell/gcc-9.3.0/votca-csg-stable-7slgbunnjcw6657pwdjeshozxpfzi3d5/share/votca/scripts/invers >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > The resulting CG table potential is zero for all the distances. >> >>> >> >> The integrate script will only act on the first valid point, >> >>> >> >> usually >> >>> >> >> marked with "i" in the last column of the force table. >> >>> >> >> So that might be the problem. Otherwise send us the force table >> >>> >> >> and we >> >>> >> >> can have a look as well. >> >>> >> >> >> >>> >> >> Christoph >> >>> >> >> >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > Looking forward to your feedback, >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > Thanks, >> >>> >> >> > >> >>> >> >> > Mohsen >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > >> >>> >> >> > On Thu, Jul 15, 2021 at 7:02 PM Christoph Junghans >> >>> >> >> > <[email protected]> wrote: >> >>> >> >> >> >> >>> >> >> >> Can you run "spack cd -b votca-csg@stable" and look for a .log >> >>> >> >> >> file in there? >> >>> >> >> >> >> >>> >> >> >> Christoph >> >>> >> >> >> >> >>> >> >> >> On Thu, Jul 15, 2021 at 2:42 PM Mohsen Farshad >> >>> >> >> >> <[email protected]> wrote: >> >>> >> >> >> > >> >>> >> >> >> > On the cluster, the run is not ending now. In my own machine, >> >>> >> >> >> > it says: >> >>> >> >> >> > >> >>> >> >> >> > ==> Error: votca-csg-stable-t3g3evics7o4vvqtxxunsnx2p67u56bg: >> >>> >> >> >> > Package was not installed >> >>> >> >> >> > >> >>> >> >> >> > ==> Error: Installation request failed. Refer to reported >> >>> >> >> >> > errors for failing package(s). >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> > The last comment on the cluster is following: >> >>> >> >> >> > >> >>> >> >> >> > [+] >> >>> >> >> >> > /home/tuo98996/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gromacs-2019.6-xtfitykzurvzarvflpj2v6cu3wywr5fc >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> > >> >>> >> >> >> > On Thu, Jul 15, 2021 at 4:38 PM Christoph Junghans >> >>> >> >> >> > <[email protected]> wrote: >> >>> >> >> >> >> >> >>> >> >> >> >> On Thu, Jul 15, 2021 at 2:34 PM Mohsen Farshad >> >>> >> >> >> >> <[email protected]> wrote: >> >>> >> >> >> >> > >> >>> >> >> >> >> > Hi Christoph, >> >>> >> >> >> >> > >> >>> >> >> >> >> > After cloning Spack I inserted the following commands on >> >>> >> >> >> >> > my own machine and the cluster, but neither machines were >> >>> >> >> >> >> > able to successfully complete the installation after a >> >>> >> >> >> >> > relatively long time. >> >>> >> >> >> >> > >> >>> >> >> >> >> > git clone https://github.com/spack/spack.git spack >> >>> >> >> >> >> > source spack/share/spack/setup-env.sh >> >>> >> >> >> >> > spack install votca-csg@stable >> >>> >> >> >> >> > >> >>> >> >> >> >> > Do you think there is something wrong with the compiler or >> >>> >> >> >> >> > I am missing some commands and installation is more >> >>> >> >> >> >> > complicated than I am thinking of? >> >>> >> >> >> >> >> >>> >> >> >> >> Can you post the error message? >> >>> >> >> >> >> >> >>> >> >> >> >> Christoph >> >>> >> >> >> >> > >> >>> >> >> >> >> > I have made sure the Spack is updated. >> >>> >> >> >> >> > >> >>> >> >> >> >> > Looking forward to hearing from you, >> >>> >> >> >> >> > >> >>> >> >> >> >> > Thanks, >> >>> >> >> >> >> > Mohsen >> >>> >> >> >> >> > >> >>> >> >> >> >> > On Sat, Jul 10, 2021 at 10:01 AM Christoph Junghans >> >>> >> >> >> >> > <[email protected]> wrote: >> >>> >> >> >> >> >> >> >>> >> >> >> >> >> On Fri, Jul 9, 2021 at 3:52 PM Christoph Junghans >> >>> >> >> >> >> >> <[email protected]> wrote: >> >>> >> >> >> >> >> > >> >>> >> >> >> >> >> > On Fri, Jul 9, 2021 at 3:42 PM Mohsen Farshad >> >>> >> >> >> >> >> > <[email protected]> wrote: >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Hi Votca developers, >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Is there a way to solve this issue without the need >> >>> >> >> >> >> >> > > for installation of "votca@stable" using spack? >> >>> >> >> >> >> >> > Not really, we really have to make a 2021.1 release and >> >>> >> >> >> >> >> > bump the spackage. >> >>> >> >> >> >> >> > Alternatively, you could apply the code change of the >> >>> >> >> >> >> >> > patch >> >>> >> >> >> >> >> > (https://github.com/votca/tools/commit/6bb7e35ba7d1a31247eafb323be2777ec0439cfe) >> >>> >> >> >> >> >> > manually. >> >>> >> >> >> >> >> > I also made a quick fix in spack: >> >>> >> >> >> >> >> > https://github.com/spack/spack/pull/24815 >> >>> >> >> >> >> >> > Once that is merged, you should be good to go. >> >>> >> >> >> >> >> The fix is part of spack now, just pull the latest >> >>> >> >> >> >> >> version of spack >> >>> >> >> >> >> >> and everything should be fine. >> >>> >> >> >> >> >> >> >>> >> >> >> >> >> > >> >>> >> >> >> >> >> > Christoph >> >>> >> >> >> >> >> > >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Thanks, >> >>> >> >> >> >> >> > > Mohsen >> >>> >> >> >> >> >> > > ---------- Forwarded message --------- >> >>> >> >> >> >> >> > > From: [email protected] <Unknown> >> >>> >> >> >> >> >> > > Date: Thursday, July 8, 2021 at 6:09:31 PM UTC-4 >> >>> >> >> >> >> >> > > Subject: C++ Compiler issue >> >>> >> >> >> >> >> > > To: [email protected] <Unknown> >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Hi Votca developers, >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > My question: C++ Compiler issue: I am trying to >> >>> >> >> >> >> >> > > install VOTCA on a supercomputer using spack. I am >> >>> >> >> >> >> >> > > getting a C++ error. Could you please have a look at >> >>> >> >> >> >> >> > > the attached log file? I am trying to figure out what >> >>> >> >> >> >> >> > > my next steps are. >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Response from Christoph: The issue you found is >> >>> >> >> >> >> >> > > already fixed (see >> >>> >> >> >> >> >> > > https://github.com/votca/tools/pull/361), but not >> >>> >> >> >> >> >> > > part of a release >> >>> >> >> >> >> >> > > yet. >> >>> >> >> >> >> >> > > You can install "votca@stable" using spack to get the >> >>> >> >> >> >> >> > > fix. >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Apologies for the test email. >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > Thank you >> >>> >> >> >> >> >> > > Akash >> >>> >> >> >> >> >> > > >> >>> >> >> >> >> >> > > -- >> >>> >> >> >> >> >> > > 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. >> >>> 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https://groups.google.com/d/msgid/votca/CAAbE4DpAJGCt-_E9RLcOQOA8QQ0jDcsm4AyHtHVfGN4JMZiqdA%40mail.gmail.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/CAHG27e4cEtmjOuKO3QEMgoHsZSyAJ%3Dp5%2BPS2bihs25p6S%3DkZSA%40mail.gmail.com. >> >>> >> >> >> > >> >>> >> >> >> > -- >> >>> >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup >> >>> >> >> 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>> To view this discussion on the web visit >> >>> >> >> >> https://groups.google.com/d/msgid/votca/CAHG27e6UhCYcqbPEb5tNk7E4dS6-4OZGzmtA9tjc7zUNsAcg2A%40mail.gmail.com. >> >>> >> >> > >> >>> >> >> > -- >> >>> >> >> > 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/CAAbE4DqTUn3QnuN1QFwb6UBnouvgbFzAJWfb9YeuL8sPNc7LvQ%40mail.gmail.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/CAHG27e67gFfpCoCrSE3LqRUd_JJkxhzrX%2BiZjaXqWPZL6KSTXQ%40mail.gmail.com. >> >>> >> > >> >>> >> > >> >>> >> > >> >>> >> > -- >> >>> >> > Mohsen Farshad >> >>> >> > Ph.D. Chemistry >> >>> >> > University of Maine >> >>> >> > >> >>> >> > -- >> >>> >> > 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/CAAbE4Dr9PXU%3D7j4%3D0TP-azBAHucna2WoWpZxz%3DCGqReCrGnaFA%40mail.gmail.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/CAHG27e43wNAE%2BD_a4NhA9sCmJT8O8rMd4JpTW-fHrHBU0oOLAg%40mail.gmail.com. >> >>> > >> >>> > -- >> >>> > 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/CAAbE4Doyh8wWXaPFoYxHtMPdnrMDA%2BjtBhnPmY3nE9X60asS2g%40mail.gmail.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/CAHG27e5X1WAuY55LbM3_o5JP2ubHRgJexuHoO0_89bn2YcXvzw%40mail.gmail.com. >> >> >> >> >> >> >> >> -- >> >> Mohsen Farshad >> >> Ph.D. Chemistry >> >> University of Maine >> > >> > >> > >> > -- >> > Mohsen Farshad >> > Ph.D. Chemistry >> > University of Maine >> > >> > -- >> > 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/CAAbE4DpT89%2BR7m3%3DoFnT_JiEtV6Kx%3DuNSqohEZ5AW8bEBiFygg%40mail.gmail.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/CAHG27e6UmuWsd0XJ0NBE6McMTgsYPArPRDNo5OySir-jpAJNYQ%40mail.gmail.com. > > > > -- > Mohsen Farshad > Ph.D. Chemistry > University of Maine > > -- > 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/CAAbE4DpX7MN5NOxQC5SBbQfKESFyVt0iL_jb0sD4%3DVb3%2BMh%2B6w%40mail.gmail.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/CAHG27e6FpEd1X1WGSAMsp__Sj62-%2Bu_d%2BxVgOhRV1am_LDQOcg%40mail.gmail.com.
