On Mon, Jun 5, 2023 at 6:17 AM Kankana Bhattacharjee < [email protected]> wrote:
> Dear Sir, > > This is the Fatal error obtained from inverse.log file: > > > > *Fatal error:The group cutoff scheme has been removed since GROMACS 2020. > Please use theVerlet cutoff scheme.* > That is right to use tabulated interactions you will to use gromacs 2019 (or lammps). VOTCA also prints a warning about that issue then you build it. Status of tables in newer gromacs versions here: https://gitlab.com/gromacs/gromacs/-/issues/1347, but unfortunately not much has moved. Christoph > > Thanks & Regards > Kankana Bhattacharjee > > > > > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> > 06/05/23, > 05:46:29 PM > > On Mon, Jun 5, 2023 at 5:32 PM Christoph Junghans <[email protected]> > wrote: > >> >> >> On Sun, Jun 4, 2023, 23:15 Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> Dear Sir, >>> >>> RDF for A-A, B-B, A-B computed from atomistic simulation using csg_stat >>> tool. Now, I am doing ibi method. But, error is coming during step 1 like >>> this: >>> Appending to existing logfile inverse.log >>> We are doing Method: ibi >>> step 0 is already done - skipping >>> Doing iteration 1 (dir step_001) >>> Simulation with gromacs >>> Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated >>> interactions only work with Group cutoff-scheme! >>> >>> ################################################################################################################## >>> # >>> # >>> # ERROR: >>> # >>> # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o >>> topol.tpr -c conf.gro' failed # >>> # For details see the logfile >>> /mnt/c/Users/KANKANA/Downloads/votca/csg-tutorials/propane/ibi-kankana/inverse.log >>> # >>> >> >> Please look up and post the detailed error message from inverse.log. >> >> >> # >>> # >>> >>> ################################################################################################################## >>> Terminated >>> >>> Kindly help me with this. >>> >>> Thanks & Regards >>> kankana Bhattacharjee >>> >>> >>> >>> >>> [image: Mailtrack] >>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>> Sender >>> notified by >>> Mailtrack >>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>> 06/05/23, >>> 10:44:51 AM >>> >>> On Sat, Jun 3, 2023 at 8:42 PM Christoph Junghans <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee < >>>> [email protected]> wrote: >>>> >>>>> Thank you sir. But IBI would be for multiple propane molecules. Isn't >>>>> it ? It won't be for single propane i think >>>>> >>>> Yes, IBI (and IMC and RE) are for multiple molecules. >>>> >>>> >>>>> >>>>> On Sat, Jun 3, 2023, 19:47 Christoph Junghans <[email protected]> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Sir, i performed atomistic simulation of single propane in vaccum. >>>>>>> But, if we use multiple propane simulation in vaccum, then csg_stat can >>>>>>> give RDF which can be compared with RDF of ibi/imc methods ? >>>>>>> >>>>>> The single molecule in vacuum is a common separation strategy to >>>>>> determine the intertra molecular interactions. In short get the bonded >>>>>> interactions from BI for the single chain run and then run IBI for the >>>>>> non-bonded interactions. >>>>>> see the Tschoep paper from 1998 ( >>>>>> https://www.votca.org/csg/bibliography.html#tschoep-1998) >>>>>> >>>>>> I want to know how to choose which method (ibi, imc) would be >>>>>>> accurate to give accurate structural properties? >>>>>>> >>>>>> That depends on the system. IBI, IMC & Re are all structure-based >>>>>> methods and try to reproduce the structure. >>>>>> Usually IBI is more robust, but needs more iterations. But IMC >>>>>> converges faster, but needs longer iterations. Marvin (who is on the >>>>>> mailing list as well) wrote an interesting paper about that recently: >>>>>> https://doi.org/10.1021/acs.jctc.2c00665 >>>>>> >>>>>> >>>>>>> On Sat, Jun 3, 2023, 09:48 Kankana Bhattacharjee < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Sir, actually it was given by professor so that, for any arbitrary >>>>>>>> molecule also I can make itp file to run CG-MD simulation. It is just >>>>>>>> for >>>>>>>> my learning purpose. >>>>>>>> >>>>>>>> Suppose, in the tutorial for CG systems topol.top file is there. >>>>>>>> Like for ibi, imc method etc. topol.top is there. But, for any unknown >>>>>>>> organic CG molecule how can one generate itp file to run CGMD >>>>>>>> simulation ? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> [image: Mailtrack] >>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>> Sender >>>>>>>> notified by >>>>>>>> Mailtrack >>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>> 06/03/23, >>>>>>>> 09:45:05 AM >>>>>>>> >>>>>>>> On Sat, Jun 3, 2023 at 9:42 AM Christoph Junghans < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> Actually sir, it was asked me to prepare propane.itp (for CG). >>>>>>>>>> >>>>>>>>> Sorry, can you explain a bit more why you need an itp file? All >>>>>>>>> the files (except for the potentials) are in the tutorial already. >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> [image: Mailtrack] >>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>> Sender >>>>>>>>>> notified by >>>>>>>>>> Mailtrack >>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>> 06/03/23, >>>>>>>>>> 08:29:51 AM >>>>>>>>>> >>>>>>>>>> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee < >>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Dear Sir, >>>>>>>>>>>> >>>>>>>>>>>> I have done boltzmann inversion of propane. now, for getting >>>>>>>>>>>> nonbonded parameters what protocol should I follow ? Because, my >>>>>>>>>>>> aim is to >>>>>>>>>>>> generate GROMACS compatible itp file for CG propane so that, can >>>>>>>>>>>> perform >>>>>>>>>>>> CG-MD using Votca. >>>>>>>>>>>> >>>>>>>>>>> Why can't you use the topology files from the propane tutorial? >>>>>>>>>>> >>>>>>>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi >>>>>>>>>>> I am asking because most of the CG methods VOTCA implement work >>>>>>>>>>> on tabulated potentials only. >>>>>>>>>>> >>>>>>>>>>> Christoph >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Thanks & Regards >>>>>>>>>>>> Kankana Bhattacharjee >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>> Sender >>>>>>>>>>>> notified by >>>>>>>>>>>> Mailtrack >>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>> 06/03/23, >>>>>>>>>>>> 12:00:35 AM >>>>>>>>>>>> >>>>>>>>>>>> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans < >>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Forgot to CC the mailing list, so here is the answer for >>>>>>>>>>>>> others. >>>>>>>>>>>>> >>>>>>>>>>>>> ---------- Forwarded message --------- >>>>>>>>>>>>> From: Christoph Junghans <[email protected]> >>>>>>>>>>>>> Date: Fri, Jun 2, 2023 at 8:22 AM >>>>>>>>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files: >>>>>>>>>>>>> To: Kankana Bhattacharjee <[email protected]> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Sir, after boltzmann inversion, bond.dist.ib, angle.dist.ib >>>>>>>>>>>>>> and bond.pot.ib, angle.pot.ib (after using tab command)files >>>>>>>>>>>>>> generated. So, >>>>>>>>>>>>>> where will I get sigma, epsilon values >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> I am not a 100% sure what you mean. >>>>>>>>>>>>> >>>>>>>>>>>>> When you use nbfunc=1 and comb-rule=1, the sigma and epsilon >>>>>>>>>>>>> column in the atomtypes block are actually the C6 and C12 >>>>>>>>>>>>> parameters (i.e. >>>>>>>>>>>>> the prefactor of 1/r**6 and 1/r**12). >>>>>>>>>>>>> But if you then use tables (vdwtype = user in the mdp file), >>>>>>>>>>>>> 1/r**6 and 1/r**12 gets replaced with the function from files you >>>>>>>>>>>>> provided >>>>>>>>>>>>> (e.g. obtained by boltzmann inversion) And hence in VOTCA we just >>>>>>>>>>>>> set >>>>>>>>>>>>> C6=C12=1, so that the table is used unmodified. >>>>>>>>>>>>> >>>>>>>>>>>>> Hope that helps, >>>>>>>>>>>>> >>>>>>>>>>>>> Christoph >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>> Sender >>>>>>>>>>>>>> notified by >>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>> 06/02/23, >>>>>>>>>>>>>> 07:34:36 PM >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans < >>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Sir, I would like to know how sigma, epsilon and default >>>>>>>>>>>>>>>> section was decided fpr CG-MD simulation ? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> no sigma and epsilon, it is all tabulated interactions. >>>>>>>>>>>>>>> see >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/grompp.mdp#L73 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> and those tables you get from boltzmann inversion (or force >>>>>>>>>>>>>>> matching). >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ---------- Forwarded message --------- >>>>>>>>>>>>>>>> From: Christoph Junghans <[email protected]> >>>>>>>>>>>>>>>> Date: Fri, Jun 2, 2023 at 7:10 PM >>>>>>>>>>>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files: >>>>>>>>>>>>>>>> To: Kankana Bhattacharjee <[email protected] >>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 3:40 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Dear Sir, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I would like to know that, in votca beads are defined >>>>>>>>>>>>>>>>> using "A, B" etc. But, how to understand what type of bead it >>>>>>>>>>>>>>>>> is i.e, >>>>>>>>>>>>>>>>> polar, aploar, charged etc. Using A, B beads can anyone run >>>>>>>>>>>>>>>>> GROMACS MD >>>>>>>>>>>>>>>>> simulation ? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> In the topol.top of the coarse grained simulation you can >>>>>>>>>>>>>>>> set the charge, e.g. see: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/topol.top#L5_L8 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks & Regards >>>>>>>>>>>>>>>>> Kankana Bhattacharjee >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>> 06/02/23, >>>>>>>>>>>>>>>>> 03:05:36 PM >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 11:06 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Dear Sir, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I have included the individual bond section in >>>>>>>>>>>>>>>>>> propane.xml file. Now, distribution is generating. >>>>>>>>>>>>>>>>>> But, for getting non-bonded parameters, which procedure >>>>>>>>>>>>>>>>>> should I have to follow ? I can use either Force Matching or >>>>>>>>>>>>>>>>>> Iterative >>>>>>>>>>>>>>>>>> methods to get non-bonded parameters. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>> 06/02/23, >>>>>>>>>>>>>>>>>> 11:03:20 AM >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 9:49 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Dear Sir, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I used this command line for bonded distribution: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> csg_boltzmann --top topol.tpr --trj traj.trr --cg >>>>>>>>>>>>>>>>>>> propane.xml < boltzmann_cmds >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> After that, got average bond length and angle >>>>>>>>>>>>>>>>>>> distribution. And, bond section is already present in my >>>>>>>>>>>>>>>>>>> propane.xml file. >>>>>>>>>>>>>>>>>>> But, still dint get any plottable bond1.dist.ib and >>>>>>>>>>>>>>>>>>> bond2.dist.ib files. >>>>>>>>>>>>>>>>>>> I am attaching the files here. >>>>>>>>>>>>>>>>>>> Please kindly help me >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Thanks & Regards >>>>>>>>>>>>>>>>>>> Kankana Bhattacharjee >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>> 06/02/23, >>>>>>>>>>>>>>>>>>> 09:37:49 AM >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:26 AM Christoph Junghans < >>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Thu, Jun 1, 2023 at 5:22 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Dear Sir, >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> I am trying to generate the histogram of bonded >>>>>>>>>>>>>>>>>>>>> distribution and convert into the boltzmann inverted >>>>>>>>>>>>>>>>>>>>> potential for single >>>>>>>>>>>>>>>>>>>>> propane which is given in the tutorial. Since, in case of >>>>>>>>>>>>>>>>>>>>> CG propane two >>>>>>>>>>>>>>>>>>>>> bond length is present (A1-B1 and B1-A2) which is >>>>>>>>>>>>>>>>>>>>> mentioned in the >>>>>>>>>>>>>>>>>>>>> propane.xml file and similarly one angle. So, I am not >>>>>>>>>>>>>>>>>>>>> understanding how >>>>>>>>>>>>>>>>>>>>> can I generate distribution of every bond of propane >>>>>>>>>>>>>>>>>>>>> molecule. I have >>>>>>>>>>>>>>>>>>>>> performed short 5 ps run of single propane molecule. When >>>>>>>>>>>>>>>>>>>>> I am adding the >>>>>>>>>>>>>>>>>>>>> line in boltzmann.cmds as: >>>>>>>>>>>>>>>>>>>>> hist bond1.dist.ib *:bond1:* >>>>>>>>>>>>>>>>>>>>> hist bond2.dist.ib *:bond2:*, then no plottable >>>>>>>>>>>>>>>>>>>>> bond1.dist.ib/bond2.dist.ib is generating. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> If you don't want to average over the 2 bonds the >>>>>>>>>>>>>>>>>>>> easiest way to do that is to add another bond block here: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/propane.xml#L34_L40 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> the names should be "bond1" and "bond2" for your >>>>>>>>>>>>>>>>>>>> application above. >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> And then run csg_stat (or csg_boltzmann): >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/run.sh#L22 >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> There is >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> My aim is to generate the every bond length histogram >>>>>>>>>>>>>>>>>>>>> Please provide me the suggestions. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks & Regards >>>>>>>>>>>>>>>>>>>>> Kankana Bhattacharjee >>>>>>>>>>>>>>>>>>>>> Ph. D. Scholar >>>>>>>>>>>>>>>>>>>>> Department of Chemistry >>>>>>>>>>>>>>>>>>>>> Ashoka University >>>>>>>>>>>>>>>>>>>>> Sonipat, Haryana >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>> 06/01/23, >>>>>>>>>>>>>>>>>>>>> 04:51:51 PM >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 10:45 AM Christoph Junghans < >>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Tue, May 30, 2023 at 10:46 PM Kankana >>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Ok sir. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I have tried to perform boltzmann inversion after >>>>>>>>>>>>>>>>>>>>>>> short (5 ps) atomistic MD run of propane. I am >>>>>>>>>>>>>>>>>>>>>>> attaching the corresponding >>>>>>>>>>>>>>>>>>>>>>> grompp.mdp file of the atomistic run, distributed >>>>>>>>>>>>>>>>>>>>>>> bonded potential files, >>>>>>>>>>>>>>>>>>>>>>> and boltzmann inverted bonded potential files. But, not >>>>>>>>>>>>>>>>>>>>>>> understanding how >>>>>>>>>>>>>>>>>>>>>>> these potential are helping in generating the itp file >>>>>>>>>>>>>>>>>>>>>>> of CG propane. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Well once you have the inverted potentials you can >>>>>>>>>>>>>>>>>>>>>> use them in the CG run, *.pot is the VOTCA format, which >>>>>>>>>>>>>>>>>>>>>> you have to >>>>>>>>>>>>>>>>>>>>>> convert to xvg (see >>>>>>>>>>>>>>>>>>>>>> https://www.votca.org/csg/preparing.html#exporting-the-table >>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> the table_a1 (a1 for Angle 1) and table_b1 (b1 for >>>>>>>>>>>>>>>>>>>>>> Bond 1) in the propane tutorials were generated this way: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> And, the thing which I understood is that, boltzmann >>>>>>>>>>>>>>>>>>>>>>> inversion is used for getting all atom inverted >>>>>>>>>>>>>>>>>>>>>>> potential and force >>>>>>>>>>>>>>>>>>>>>>> matching is used for getting non-bonded potentials. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> For you can use iterative boltzmann inversion for the >>>>>>>>>>>>>>>>>>>>>> non-bonded interactions. >>>>>>>>>>>>>>>>>>>>>> (Force-matching works for bonded interactions as >>>>>>>>>>>>>>>>>>>>>> well, but VOTCA has implemented that) >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> CG propane itp (topol.top) file is available in >>>>>>>>>>>>>>>>>>>>>>> ibi/imc methods part of votca. Can it be supplied in >>>>>>>>>>>>>>>>>>>>>>> performing CG-MD >>>>>>>>>>>>>>>>>>>>>>> simulation using GROMACS ? >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> If you run the propane tutorial after a couple of >>>>>>>>>>>>>>>>>>>>>> steps you will have some tabulated potential that you >>>>>>>>>>>>>>>>>>>>>> can use for CG-MD. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>>>> 05/31/23, >>>>>>>>>>>>>>>>>>>>>>> 10:12:10 AM >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 10:10 AM Christoph Junghans < >>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Tue, May 30, 2023 at 10:33 PM Kankana >>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Thank you sir. I would like to know, how can one >>>>>>>>>>>>>>>>>>>>>>>>> get gromacs compatible itp file for a Coarse grained >>>>>>>>>>>>>>>>>>>>>>>>> model using votca ? >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> It is all tabulated interaction, hence no itp files. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> And the interactions are determined by IBI, IMC or >>>>>>>>>>>>>>>>>>>>>>>> Force Matching, whatever you prefer. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>>>>>> 05/31/23, >>>>>>>>>>>>>>>>>>>>>>>>> 10:02:22 AM >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 9:58 AM Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Sun, May 28, 2023 at 10:13 PM Kankana >>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks a lot sir for your kind help. >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> I have gone through the topol.top file of spce >>>>>>>>>>>>>>>>>>>>>>>>>>> and propane model using ibi method. I have doubts, >>>>>>>>>>>>>>>>>>>>>>>>>>> how did you define the >>>>>>>>>>>>>>>>>>>>>>>>>>> mass of the beads, charge, bond and angle between >>>>>>>>>>>>>>>>>>>>>>>>>>> beads in topol.top file >>>>>>>>>>>>>>>>>>>>>>>>>>> of the CG model ? >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> For a center of mass mapping it is just the sum >>>>>>>>>>>>>>>>>>>>>>>>>> of the masses (and charges), but of course you can >>>>>>>>>>>>>>>>>>>>>>>>>> do other mappings, too. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> In general making a coarse-grained model is more >>>>>>>>>>>>>>>>>>>>>>>>>> art than science. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>>>>>>>>>>>>> 05/29/23, >>>>>>>>>>>>>>>>>>>>>>>>>>> 09:41:28 AM >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, May 26, 2023 at 9:15 PM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, May 25, 2023 at 7:23 AM Kankana >>>>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee >>>>>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > Dear Sir, >>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am learning votca. Now, I have done spce >>>>>>>>>>>>>>>>>>>>>>>>>>>> water model atomistic md run. In the >>>>>>>>>>>>>>>>>>>>>>>>>>>> spce/atomistic foolder, grompp.mdp >>>>>>>>>>>>>>>>>>>>>>>>>>>> contains integrator as "sd" . And, I used this >>>>>>>>>>>>>>>>>>>>>>>>>>>> settings for short MD run. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Then, used csg_tool to compute rdf of CG-CG beads >>>>>>>>>>>>>>>>>>>>>>>>>>>> and compared with CG-CG >>>>>>>>>>>>>>>>>>>>>>>>>>>> with ibi. Then, I dint understand the "Running >>>>>>>>>>>>>>>>>>>>>>>>>>>> ibi" part of the spce model. >>>>>>>>>>>>>>>>>>>>>>>>>>>> It has been asked to reduce the number of MD steps >>>>>>>>>>>>>>>>>>>>>>>>>>>> in grompp.mdp and adjust >>>>>>>>>>>>>>>>>>>>>>>>>>>> the equilibration time in the settings.xml file. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Exactly how to adjust this >>>>>>>>>>>>>>>>>>>>>>>>>>>> and why ? I have skipped the "Running ibi" option. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Well, the number of MD steps is in grompp.mdp, >>>>>>>>>>>>>>>>>>>>>>>>>>>> while the equilibration >>>>>>>>>>>>>>>>>>>>>>>>>>>> time is in settings.xml. Longer run will give >>>>>>>>>>>>>>>>>>>>>>>>>>>> you smoother RDFs, and >>>>>>>>>>>>>>>>>>>>>>>>>>>> the system usually needs some time to >>>>>>>>>>>>>>>>>>>>>>>>>>>> equilibrate from the initial >>>>>>>>>>>>>>>>>>>>>>>>>>>> condition, so you don't want to pick that too >>>>>>>>>>>>>>>>>>>>>>>>>>>> short. In the tutorial >>>>>>>>>>>>>>>>>>>>>>>>>>>> we ask folks to explore these options to get >>>>>>>>>>>>>>>>>>>>>>>>>>>> some feel for statistics. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > Second;y, I did force matching part exactly. >>>>>>>>>>>>>>>>>>>>>>>>>>>> But, dint understand exactly what is happening. >>>>>>>>>>>>>>>>>>>>>>>>>>>> Like, If I want to generate >>>>>>>>>>>>>>>>>>>>>>>>>>>> gromacs compatible forcefield.itp for a coarse >>>>>>>>>>>>>>>>>>>>>>>>>>>> grained model and perform MD >>>>>>>>>>>>>>>>>>>>>>>>>>>> simulation using gromacs. THen, how can I generate >>>>>>>>>>>>>>>>>>>>>>>>>>>> ttp file for a molecule. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Force matching return a tabulated force that >>>>>>>>>>>>>>>>>>>>>>>>>>>> can then be used to run >>>>>>>>>>>>>>>>>>>>>>>>>>>> the coarse-grained simulation. Have a look at >>>>>>>>>>>>>>>>>>>>>>>>>>>> the topol.top of the >>>>>>>>>>>>>>>>>>>>>>>>>>>> spce/ibi example. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks & Regards >>>>>>>>>>>>>>>>>>>>>>>>>>>> > Kankana Bhattacharjee >>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>> > -- >>>>>>>>>>>>>>>>>>>>>>>>>>>> > 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/c6eaf8c8-1963-4772-9800-dc9d839dd0bbn%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/CAHG27e73xWx4bDHzx2AAxA%2B8OaQC%2B_6ru%2B7iACRsRWZrDJOoqQ%40mail.gmail.com >>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [image: Mailtrack] >>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>> Sender >>>>>>>>>>>>>>>> notified by >>>>>>>>>>>>>>>> Mailtrack >>>>>>>>>>>>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>>>>>>>>>>>> 06/02/23, >>>>>>>>>>>>>>>> 07:13:42 PM >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> 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/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com >>>>>>>>>>>>> <https://groups.google.com/d/msgid/votca/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>>>>>>>> . >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Christoph Junghans >>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>> >>>>>>>>>> -- >>>>>>>>> Christoph Junghans >>>>>>>>> Web: http://www.compphys.de >>>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Christoph Junghans >>>>>> Web: http://www.compphys.de >>>>>> >>>>> >>>> >>>> -- >>>> 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/CAHG27e4GYEyMk42oYqw1t8UrvWdbM%3Dc5y7vFM_W4VtafkhDxFg%40mail.gmail.com.
