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. 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.
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 ? [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 > -- 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/CAMNJFVniw6DFU45%2BU319G%3DJMBaedgHrEPvgrgx37KKvvi3WNbw%40mail.gmail.com.
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bond.pot
Description: MS-Powerpoint presentation
angle.pot
Description: MS-Powerpoint presentation
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grompp.mdp
Description: Binary data
