On Thu, Jul 22, 2021 at 10:39 AM Mohsen Farshad <[email protected]> wrote: > > Thank you very much. I am running the CG simulation using the FM potential > table obtained through the force-matching process in the force_matching > folder and grompp.mdp from the atomistic folder. I receive the below error > after the following commands: > > gmx grompp -f grompp.mdp -p topol.top -c conf_cg.gro > > gmx mdrun -table table_CG_CG.xvg > > > Fatal error: > > An atom moved too far between two domain decomposition steps > > This usually means that your system is not well equilibrated Yeah, this error basically means your system exploded, I would try to run a minimization first.
Christoph > > > I attach all the files here. > > Thanks, > Mohsen > > > > On Thu, Jul 22, 2021 at 9:05 AM Christoph Junghans <[email protected]> wrote: >> >> On Wed, Jul 21, 2021 at 8:26 PM Mohsen Farshad <[email protected]> >> wrote: >> > >> > After I run the following command: >> > >> > csg_gmxtopol --top topol.tpr --cg water.xml --out topol_cg >> > >> > the following topol_cg is generated: >> > >> > SOL 3 >> > >> > >> > >> > [atoms] >> > >> > ; nr type resnr residue atom cgnr charge mass >> > >> > 1 CG 1 RES CG 1 0.000000 18.015400 >> > >> > Is this incomplete? Is the attached spc/e topology file from the IBI >> > folder belong to the coarse-graining spc/e? If so do you have any insight >> > in regards to why the above topology file is not the same as the attached >> > file? >> Yes, it is incomplete, the help of csg_gmxtopol says it all: >> "Create skeleton for gromacs topology based on atomistic topology >> and a mapping file. File still needs to be modified by the user." >> >> IBI is basically running the cg simulation over and over again without >> knowing the potential, hence the topology from the tutorials is just >> the cg one. >> >> csg_gmxtopol can only deal with one molecule type right now (patches >> welcome), hence the generated topology is missing some block incl. >> defaults, atomtypes, system, molecules and maybe other funky things >> you want to do in the cg simulation. >> >> Please have a look at the gromacs manual on how to write a topology >> file, it is really not that hard. >> https://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html#topology-file >> >> Christoph >> >> > >> > Thanks, >> > Mohsen >> > >> > >> > >> > On Wed, Jul 21, 2021 at 9:32 PM Christoph Junghans <[email protected]> >> > wrote: >> >> >> >> >> >> >> >> On Wed, Jul 21, 2021 at 19:20 Mohsen Farshad <[email protected]> >> >> wrote: >> >>> >> >>> This means I have to use the following command to make the CG topology >> >>> file: >> >>> >> >>> "csg_gmxtopol --top topol.top --cg water.xml --out topol_CG.top" >> >>> >> >>> where water.xml and topol.top can be found in the SPC/E tutorial in the >> >>> atomistic folder. >> >>> >> >>> and for making the configuration file I can use the center of mass of >> >>> water molecules which is made by mapping command from atomistic SPC/E >> >>> using the following commands: >> >>> >> >>> echo "Mapping confout.gro to get the starting configuration for >> >>> coarse-grain >> >>> >> >>> csg_map --top topol.tpr --trj conf.gro --cg water.xml --out conf_cg.gro >> >>> >> >>> >> >>> In the same way, it is asking the user to do it in the tutorial. >> >>> >> >>> Please let me know if any of the above commands or relevant explanation >> >>> to create the topology and configuration of the CG system is wrong. >> >> >> >> All correct, you might have to check and hand-edit the generated >> >> topol.top. >> >> >> >> For spc/e you could also use the topology from the ibi tutorial. >> >> >> >> Christoph >> >>> >> >>> >> >>> Thanks, >> >>> Mohsen >> >>> >> >>> On Wed, Jul 21, 2021 at 5:25 PM Christoph Junghans <[email protected]> >> >>> wrote: >> >>>> >> >>>> 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. >> >>>> >> >>> >> >> >> >> >> > > 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/4ee1f111-852d-4526-9920-55cfe9b110e9n%40googlegroups.com. >> >>>> >> >>> >> >> >> >> >> > >> >>>> >> >>> >> >> >> >> >> > >> >>>> >> >>> >> >> >> >> >> > >> >>>> >> >>> >> >> >> >> >> > -- >> >>>> >> >>> >> >> >> >> >> > Christoph Junghans >> >>>> >> >>> >> >> >> >> >> > Web: http://www.compphys.de >> >>>> >> >>> >> >> >> >> >> >> >>>> >> >>> >> >> >> >> >> >> >>>> >> >>> >> >> >> >> >> >> >>>> >> >>> >> >> >> >> >> -- >> >>>> >> >>> >> >> >> >> >> 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/CAHG27e42Gj-VuA2sudLLec34W8J5RNuu0ocod9C8aee7jwoMEg%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/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 >> >>>> >> >>> >> >> >> > --- >> >>>> >> >>> >> >> >> > 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/CAAbE4Dq6vsiEjqxsJGoVLawnA4VwPzLaCbO7zn3Avn2xJoa5rg%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/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. >> >>> >> >>> >> >>> >> >>> -- >> >>> 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/CAAbE4DoRNR8xanjRDrxEjAzyLomyP9CYYqMngLo_3dBAFvSf6A%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/CAHG27e4P_O0e-GhHc0YFS8EbTVOWBdttib7t4W6LQrQuf6xUgQ%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/CAAbE4DoZRS_df_i-rwGQn0wwz9gXz3UmKt8gtnzib%3DrPpHZTBQ%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/CAHG27e5f1f9UkfU%3DjXuOjx%3DhBufBLMEVL1b6Dpm9rFPgFyyG6Q%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/CAAbE4DphKMo202XFNH3L7Ywh5r%3D6JP%2BBnB_TzhRmfVQPpVzVmg%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/CAHG27e5C3SM85AwMbtR8rtG2VtMrTBAzonzW5cGR99617Rx3%3Dw%40mail.gmail.com.
