On Mon, Jul 26, 2021 at 2:27 PM Mohsen Farshad <[email protected]> wrote: > > David and Christoph, > > I read the relevant parts of the pdf that David sent us. Thank you for that. > My brain neurons are getting wired up, however, I need to clarify my > understandings, therefore that would be great if you correct me if my > following interpretations are incorrect or imprecise: > > Potential table coordinate with both .gro and .ndx files. Looks at index file > for separating the potential tables and also looks at .gro for specifying the > none_bonded interactions by finding the names of particles in .gro. Not quite, really only the index group name matters, but one could name the group FOO, then the table would be called table_FOO_FOO.xvg. We just happen to name the index group that contains all CG atoms "CG". In other tutorials you will see more table, e.g. with groups A and B you will see table_A_A.xvg, table_B_B.xvg and table_A_B.xvg.
> > The user tabulated table should have a specific name like table_CG_CG that > which in this case determines the interaction between CG and CG in .gro file. > If the system has more atoms than defined in CG list then the Gromacs looks > for parameters from a default potential table called table.xvg which is in my > case nothing as the whole system is CG. It is not clear in PDF where this > table.xvg comes from if it is not defined by USER. It might be that newer gromacs versions don't need table.xvg anymore, but back in gromacs-5 times, gromacs could not figure out if all combinations of energy groups were covered by the tables given. Just imagine you have N index groups, then you need N*(N-1)/2 + N tables, so table.xvg is the fallback table for uncovered groups and is usually just a normal C6 /C12 LJ potential. > > The following two lines in mdp file > > Read user tables from table_CG_CG.xvg with 2501 data points. > > Tabscale = 1000 points/nm > > Read user tables from table.xvg with 1501 data points. > > Tabscale = 500 points/nm > > > The first table is specific to the CG particles and the second one is for > system particles, and because the whole system in my case is CG elements the > table.xvg will remain without any use. Therefore, it does not matter what it > contains as long as it is following the format of a Gromacs potential table. Correct. Christoph > > Thanks, > Mohsen > > > > > > > > > > > On Mon, Jul 26, 2021 at 1:56 PM 'David Rosenberger' via votca > <[email protected]> wrote: >> >> Here's a more extended explanation for tables and gromacs: >> https://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf >> It's for a very old version, but still contains all important information. >> >> Christoph Junghans schrieb am Montag, 26. Juli 2021 um 19:51:23 UTC+2: >>> >>> On Mon, Jul 26, 2021 at 11:31 AM Mohsen Farshad >>> <[email protected]> wrote: >>> > >>> > Hi Christoph, >>> > >>> > Thanks. Would you please let me know how you realize the system is using >>> > table_CG_CG.xvg rather than table.xvg for the CG system by looking at >>> > those lines in .log file? >>> You can usually see that when you create the index file, the number of >>> atoms in CG should be the same as in the "system" group. >>> >>> Christoph >>> > >>> > On Mon, Jul 26, 2021 at 1:02 PM Christoph Junghans <[email protected]> >>> > wrote: >>> >> >>> >> On Mon, Jul 26, 2021 at 10:20 AM Mohsen Farshad >>> >> <[email protected]> wrote: >>> >> > >>> >> > Thank you very much for your replies. The system is running. I checked >>> >> > what potential is the system using, here is a portion of .log file: >>> >> > >>> >> > 361 Read user tables from table_CG_CG.xvg with 2501 data points. >>> >> > >>> >> > 362 Tabscale = 1000 points/nm >>> >> > >>> >> > 363 Read user tables from table.xvg with 1501 data points. >>> >> > >>> >> > 364 Tabscale = 500 points/nm >>> >> > >>> >> > 365 >>> >> > >>> >> > 366 NOTE: All elements in table table.xvg are zero >>> >> > >>> >> > >>> >> > Does "All elements in table table.xvg are zero" The table.xvg file is >>> >> > treated like a dummy file and the system is actually using >>> >> > "table_CG_CG.xvg"? >>> >> >>> >> table_CG_CG.xvg is used for all atoms between the CG and CG groups. >>> >> And table.xvg for everything else, but as everything is covered under >>> >> the CG-CG part you should be good. >>> >> >>> >> Christoph >>> >> >>> >> > >>> >> > >>> >> > >>> >> > On Mon, Jul 26, 2021 at 11:57 AM 'David Rosenberger' via votca >>> >> > <[email protected]> wrote: >>> >> >> >>> >> >> For the index file: You have to make a selection. If you press 'q' >>> >> >> the index file will be generated, with the three selections presented >>> >> >> above. >>> >> >> You have to type 'a CG' to add the CG atoms to the index file, if you >>> >> >> then press 'q' a index file with 4 selctions will be generated. >>> >> >> >>> >> >> Maybe it's advisory for you to go carefully through a gromacs >>> >> >> tutorial and read the corresponding sections in the manual >>> >> >> before continuing. >>> >> >> >>> >> >> David Rosenberger schrieb am Montag, 26. Juli 2021 um 17:51:53 UTC+2: >>> >> >>> >>> >> >>> Gromacs 2020 doesn't support tabulated potentials. You have to >>> >> >>> switch to a older version. >>> >> >>> Maybe it's back in Gromacs 2021, but 2020 cannot be used. >>> >> >>> >>> >> >>> >>> >> >>> [email protected] schrieb am Montag, 26. Juli 2021 um 17:47:10 >>> >> >>> UTC+2: >>> >> >>>> >>> >> >>>> I forgot to mention, the system crashed with the same error. I must >>> >> >>>> be missing something very simple yet frustrating. >>> >> >>>> >>> >> >>>> On Mon, Jul 26, 2021 at 11:45 AM Mohsen Farshad >>> >> >>>> <[email protected]> wrote: >>> >> >>>>> >>> >> >>>>> When I do this "gmx make_ndx -f conf_cg.gro" I receive the >>> >> >>>>> following in the command line without any index file generated. Do >>> >> >>>>> you know the reason for this? Also I do not understand what does >>> >> >>>>> "select CG mean". >>> >> >>>>> >>> >> >>>>> gmx make_ndx -f conf_cg.gro >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> Reading structure file >>> >> >>>>> >>> >> >>>>> Going to read 0 old index file(s) >>> >> >>>>> >>> >> >>>>> Analysing residue names: >>> >> >>>>> >>> >> >>>>> There are: 2180 Water residues >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> 0 System : 2180 atoms >>> >> >>>>> >>> >> >>>>> 1 Water : 2180 atoms >>> >> >>>>> >>> >> >>>>> 2 SOL : 2180 atoms >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> nr : group '!': not 'name' nr name 'splitch' nr Enter: list groups >>> >> >>>>> >>> >> >>>>> 'a': atom '&': and 'del' nr 'splitres' nr 'l': list residues >>> >> >>>>> >>> >> >>>>> 't': atom type '|': or 'keep' nr 'splitat' nr 'h': help >>> >> >>>>> >>> >> >>>>> 'r': residue 'res' nr 'chain' char >>> >> >>>>> >>> >> >>>>> "name": group 'case': case sensitive 'q': save and quit >>> >> >>>>> >>> >> >>>>> 'ri': residue index >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> > >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> However, I copied the index file from IBI folder to the current >>> >> >>>>> folder and ran the following commands: >>> >> >>>>> >>> >> >>>>> gmx grompp -f grompp.mdp -c em.gro -n index.ndx >>> >> >>>>> >>> >> >>>>> gmx mdrun -table >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> Would you please let me know how should I look for table in >>> >> >>>>> md.log. I could not find any.xvg file in the md.log. I attach it >>> >> >>>>> here. >>> >> >>>>> >>> >> >>>>> Thanks, >>> >> >>>>> Mohsen >>> >> >>>>> >>> >> >>>>> >>> >> >>>>> On Mon, Jul 26, 2021 at 11:16 AM 'David Rosenberger' via votca >>> >> >>>>> <[email protected]> wrote: >>> >> >>>>>> >>> >> >>>>>> Hi Mohsen, >>> >> >>>>>> >>> >> >>>>>> I used your files. Did you re-run grompp? >>> >> >>>>>> >>> >> >>>>>> Here's what I did: >>> >> >>>>>> gmx make_ndx -f conf_cg.gro and then for selection: a 'CG'. >>> >> >>>>>> >>> >> >>>>>> Then gmx grompp -f conf_cg.gro -n index.ndx. >>> >> >>>>>> >>> >> >>>>>> Then gmx mdrun -table. >>> >> >>>>>> >>> >> >>>>>> If you do that, then check what is written in the md.log file and >>> >> >>>>>> see which table file is used. >>> >> >>>>>> >>> >> >>>>>> If it crashes, it doesn't use the correct table file. 'table.xvg' >>> >> >>>>>> is just a dummy file, which gromacs is looking for. >>> >> >>>>>> It then automatically takes table_CG_CG.xvg for the CG_CG >>> >> >>>>>> interaction defined in energy groups. >>> >> >>>>>> >>> >> >>>>>> Best, >>> >> >>>>>> David >>> >> >>>>>> >>> >> >>>>>> >>> >> >>>>>> [email protected] schrieb am Montag, 26. Juli 2021 um 16:34:34 >>> >> >>>>>> UTC+2: >>> >> >>>>>>> >>> >> >>>>>>> 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. >>> >> >>>>>>>>>>>> >>> >> >>>>>>>>>>>> -- >>> >> >>>>>>>>>>>> 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. >>> >> >>>>>>>>>>> >>> >> >>>>>>>>>>> >>> >> >>>>>>>>>>> >>> >> >>>>>>>>>>> -- >>> >> >>>>>>>>>>> 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. >>> >> >>>>>>>>> >>> >> >>>>>>>>> >>> >> >>>>>>>>> >>> >> >>>>>>>>> -- >>> >> >>>>>>>>> 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. >>> >> >>>>>>> >>> >> >>>>>>> >>> >> >>>>>>> >>> >> >>>>>>> -- >>> >> >>>>>>> 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/e7b07df5-4862-47ef-b33c-ca644d0c07d3n%40googlegroups.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/8aa80bd5-a159-4bd8-80f0-3b25b998addan%40googlegroups.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/CAAbE4Dr8TqRGpcxp7Va%3Dxdjai_B6SJ5jpkfZOJwO9hFJ06UPqw%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/CAHG27e7uiCt%2BY0eD6gT5wJk_esM7jPv0VQTCdNfqV8eCUea%2BqQ%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/CAAbE4DpxnNcK2AOntm-EYQUOzGjq40QeF1u%3D-%3D38KqGd%3Dshw-Q%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/4a6a5db5-c89f-4374-88bc-70062d2698cfn%40googlegroups.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/CAAbE4Drv-RM0rV9mcabnLXS-Eh9L5LXNF5uLcwj_iDk%3D7Z9h0w%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/CAHG27e5Stek%3DKr2VKiwTPP4AENq1fRnr%3DNrP-hFb-FxD-Qg_YQ%40mail.gmail.com.
