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. 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