gromacs-2020 and never should error out if you are using cutoff_scheme=group. When using csg_inverse VOTCA will automatically add that line to the mdp file, hence it is not in the spce tutorials mdp file.
Christoph On Mon, Jul 26, 2021 at 9:57 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. -- 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/CAHG27e4twx3Am8YiHzX_CK60d53nmbg%3DhX%3Dp2vRHmAhwuo_Rkg%40mail.gmail.com.
