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 -- 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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