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? 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.
