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 -- 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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