On Fri, Jul 23, 2021, 09:03 Mohsen Farshad <[email protected]> wrote:
> Hi Christoph, > > I use the following .mdp gromacs script adjusted from the gromacs tutorial > to minimize the our CS system: > > 1 ; minim.mdp - used as input into grompp to generate em.tpr > > 2 ; Parameters describing what to do, when to stop and what to save > > 3 integrator = steep ; Algorithm (steep = steepest descent > minimization) > > 4 emtol = 1000.0 ; Stop minimization when the maximum > force < 1000.0 kJ/mol/nm > > 5 emstep = 0.001 ; Minimization step size > > 6 nsteps = 100000 ; Maximum number of (minimization) steps > to perform > > 7 > > 8 ; Parameters describing how to find the neighbors of each atom and > how to calculate the interactions > > 9 nstlist = 1 ; Frequency to update the neighbor list > and long range forces > > 10 ns_type = grid ; Method to determine neighbor list > (simple, grid) > > 11 coulombtype = Reaction-Field ; Treatment of long range > electrostatic interactions > > 12 rcoulomb = 1.0 ; Short-range electrostatic cut-off > > 13 rvdw = 1.0 ; Short-range Van der Waals cut-off > > 14 pbc = xyz ; Periodic Boundary Conditions in all 3 > dimensions > > > and I get the following error: > > > Steepest Descents converged to machine precision in 8003 steps, > > but did not reach the requested Fmax < 1000. > > > Is this the right way to minimize the system? If so is there something > wrong with the initial configuration? > The mdp looks right! The force limit isn't super important as long as it is converted. I would go ahead now and give the cg run another try with the minimized configuration as starting point. Christoph > Thanks, > Mohsen > > > On Thu, Jul 22, 2021 at 2:41 PM Christoph Junghans <[email protected]> > wrote: > >> 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 >> . >> > > > -- > 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/CAAbE4DqyhA-iO3Grzmt3aRJz8BkS2M%2BqF2vcuJYAjmvxxvDgRg%40mail.gmail.com > <https://groups.google.com/d/msgid/votca/CAAbE4DqyhA-iO3Grzmt3aRJz8BkS2M%2BqF2vcuJYAjmvxxvDgRg%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- 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/CAHG27e7_vk5jx4fjmfrpy%3DnKQXKzB1cjoZQZemE48V41gys4SA%40mail.gmail.com.
