Hi David, Thank you. I did not realized that those lines indicate the Gromacs is not reading the potential table.
Did you use the following command to generate the index file: gmx make_ndx -f em.gro -o index.ndx I added table.xvg from IBI to and changed the command to gmx mdrun with both tables in the current folder. I added the cutoff_scheme=group to grompp.mpd but still got the same error with different versions of gromacs. Would you please send me the files that you used to run the system? Also, for clarification, I want to use force-matching potential to run the system rather than IBI potential. Looking forward to hearing from you, Thanks, Mohsen On Mon, Jul 26, 2021 at 4:01 AM 'David Rosenberger' via votca < [email protected]> wrote: > Hi Mohsen, > by having a look at the md.log file, I think the issue is the following: > -------- > generated table with 1186 data points for RF-zero. > Tabscale = 500 points/nm > Generated table with 1186 data points for LJ6. > Tabscale = 500 points/nm > Generated table with 1186 data points for LJ12. > Tabscale = 500 points/nm > -------- > Gromacs does not read your table properly, but insteads generates a > generic one. > > Could you copy the table.xvg file from e.g. the spce/ibi example to your > working directory and run "mdrun -table", instead of "mdrun -table > table_CG_CG.xvg? > Note: You need both files: table.xvg and table_CG_CG.xvg. > > I tested your files with gromacs 2019v2, and it runs without any problems. > > Though I had to generate an index file containing the "CG" atoms, and I > had to add "cutoff-scheme=group" to the mdp file. > > Best, > David > [email protected] schrieb am Sonntag, 25. Juli 2021 um 20:47:38 UTC+2: > >> Hi David, >> >> Thanks for the informative explanation on the equation of motion, I had >> not realized that. >> >> I changed the integrator from md to sd and confronted a similar error: >> >> Fatal error: >> >> An atom moved too far between two domain decomposition steps >> >> This usually means that your system is not well equilibrated >> >> >> Thanks, >> >> Mohsen >> >> On Sun, Jul 25, 2021 at 12:37 PM 'David Rosenberger' via votca < >> [email protected]> wrote: >> >>> Hi Mohsen, >>> >>> can you please change the integrator in the mdp file from "md" to "sd'? >>> >>> It seems you don't have a thermostat. >>> Your integrator is "md", and you set "Tcouple=no". This means you don't >>> have a thermostat. You don't need to define a thermostat if you use the >>> "sd" integrator. >>> "SD" has some friction term in the equations of motions, this has the >>> same effect as setting thermostat, given a proper value for tau_t is set. >>> For more please see the GROMACS manual. >>> >>> General remark: For coarse grained systems it is better to use >>> Langevin-type equations of motions (e.g. the SD integrator in GROMACS), as >>> you loose friction between particles due to the coarsening. >>> >>> Best, >>> David >>> >>> [email protected] schrieb am Samstag, 24. Juli 2021 um 19:51:25 >>> UTC+2: >>> >>>> Thanks. I tried to do simulation with the minimized structure using FM >>>> potential table. But the problem remains with the same following error: >>>> >>>> Fatal error: >>>> >>>> An atom moved too far between two domain decomposition steps >>>> >>>> This usually means that your system is not well equilibrated >>>> >>>> >>>> >>>> I tried different things including using IBI potential table, >>>> minimizing the minimized structure, changing the parameters in the .mdp, >>>> but none of them solved the problem. I must mention that I pretty new to >>>> the Gromacs and Votca. I attach the files here, that would be a great if >>>> you could look at the files. Are you able to run this? >>>> >>>> em.gro is the minimized structure and conf_cg.gro is the >>>> initial structure of spc/e model. >>>> >>>> Thanks, >>>> Mohsen >>>> >>>> >>>> >>>> On Fri, Jul 23, 2021 at 9:04 PM Christoph Junghans <[email protected]> >>>> wrote: >>>> >>>>> >>>>> >>>>> 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 >>>>> <https://groups.google.com/d/msgid/votca/CAHG27e7_vk5jx4fjmfrpy%3DnKQXKzB1cjoZQZemE48V41gys4SA%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> >>>> >>>> -- >>>> 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/e3e77efb-2398-40af-8cf4-8058f6583ddbn%40googlegroups.com >>> <https://groups.google.com/d/msgid/votca/e3e77efb-2398-40af-8cf4-8058f6583ddbn%40googlegroups.com?utm_medium=email&utm_source=footer> >>> . >>> >> >> >> -- >> 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/8da04045-884c-493b-ad0b-e511a45e6b1dn%40googlegroups.com > <https://groups.google.com/d/msgid/votca/8da04045-884c-493b-ad0b-e511a45e6b1dn%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- 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/CAAbE4Dr1rj9M8PFjoqO%3D39R1P%2BoOgRb%3D1%2BJht7mpB55RWBrWkA%40mail.gmail.com.
