On Thu, Jun 8, 2023, 06:29 Kankana Bhattacharjee < [email protected]> wrote:
> Sorry sir, bonded section is also there. To obtain a bond table, the used > command line is: > > csg_call --ia-type bond --ia-name XXX --options table.xml \ > convert_potential gromacs table_extrapolate.pot table.xvg > > I would like to know, in --ia-name flag, what I should I put there, would > it foolow the name which is mentioned in the propane.xml file in bonded > section (bond1, bond2) ? > Yes, it is just the same names you defined in table.xml. 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&;> > 06/08/23, > 03:57:07 PM > > On Thu, Jun 8, 2023 at 3:46 PM Kankana Bhattacharjee < > [email protected]> wrote: > >> But, sir for this process, a table.xml file is given for non-bonded >> intercations. But, how to do the same job for bonded distributions ? >> >> >> >> [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&;> >> 06/08/23, >> 03:44:48 PM >> >> On Thu, Jun 8, 2023 at 3:42 PM Christoph Junghans <[email protected]> >> wrote: >> >>> >>> >>> On Thu, Jun 8, 2023, 06:01 Kankana Bhattacharjee < >>> [email protected]> wrote: >>> >>>> Ok. Thank you sir. I understood that, table number concept i.e, >>>> table_a1.xvg, table_b1.xvg. But, how can one generate those files to supply >>>> in bonded.itp file ? I can see those table (bond1, angle1).xvg files in the >>>> ibi directory. But, how those files get generated ? >>>> >>> https://www.votca.org/csg/preparing.html#exporting-the-table >>> >>> >>>> ---------- Forwarded message --------- >>>> From: Christoph Junghans <[email protected]> >>>> Date: Thu, Jun 8, 2023 at 3:27 PM >>>> Subject: Re: [votca] Regarding-Getting-itp-files: >>>> To: Kankana Bhattacharjee <[email protected]> >>>> >>>> >>>> >>>> >>>> On Thu, Jun 8, 2023, 01:43 Kankana Bhattacharjee < >>>> [email protected]> wrote: >>>> >>>>> Dear Sir, >>>>> >>>>> I would like to know, how in the case of CG propane.itp file, I have >>>>> found that, "func type 8" is used which is tabulated functional form. And, >>>>> in the case of "func type 8", there are two parameters "table number" and >>>>> "spring constant" values. And, how two parameters (table number, spring >>>>> constant) are obtained (which is equal to 1 in topol.top file) ? Like, as >>>>> I >>>>> am doing it manually, and bonded values obtained from BI method, then how >>>>> can I mention spring constant, and table number values in bonded.itp file >>>>> ? >>>>> >>>> The spring constant is yet another number the table gets multipled >>>> with, but for BI you don't need another factor that hence we set it to 1.0! >>>> >>>> The table number is arbitrary, but needs to consistent with the files >>>> name, table_b<#>.xvg and table_a<#>.xvg. (b for bond, a for angle, see the >>>> Gromacs manual for details). >>>> >>>> Christoph >>>> >>>>> >>>>> Thanks and 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&;> >>>>> 06/08/23, >>>>> 11:08:09 AM >>>>> >>>>> On Mon, Jun 5, 2023 at 7:13 PM Kankana Bhattacharjee < >>>>> [email protected]> wrote: >>>>> >>>>>> Ok sir >>>>>> >>>>>> On Mon, Jun 5, 2023, 19:00 Christoph Junghans <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> On Mon, Jun 5, 2023 at 7:11 AM Kankana Bhattacharjee < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Ok sir. >>>>>>>> If i use CG MD only using gromacs without using votca, is it >>>>>>>> possible to do with gromacs 2020 or later version? If i don't use >>>>>>>> iterative >>>>>>>> methods >>>>>>>> >>>>>>> Well even the non-iterative methods like Boltzmann inversion and >>>>>>> Force Matching use tables. >>>>>>> You would have to fit them to a Lennard-Jones form to use Gromacs >>>>>>> 2020. >>>>>>> >>>>>>> Christoph >>>>>>> >>>>>>>> >>>>>>>> On Mon, Jun 5, 2023, 18:16 Christoph Junghans <[email protected]> >>>>>>>> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Jun 5, 2023 at 6:35 AM Kankana Bhattacharjee < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> Ok sir. What should I do to fix it ? >>>>>>>>>> >>>>>>>>> Build VOTCA against gromacs-2019. VOTCA even has an option to >>>>>>>>> build its own gromacs (BUILD_OWN_GROMACS). >>>>>>>>> >>>>>>>>> >>>>>>>>>> Is it true for all iterative methods ? >>>>>>>>>> >>>>>>>>> Yes, but of course you can always use lammps to do the 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&;> >>>>>>>>>> 06/05/23, >>>>>>>>>> 06:05:14 PM >>>>>>>>>> >>>>>>>>>> On Mon, Jun 5, 2023 at 6:04 PM Christoph Junghans < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- 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. 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