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 -- 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/CAHG27e4_7sQP1PCZwbTjuXMwEC%2BFRHa%2BfnaiD-crtssGMYoxYA%40mail.gmail.com.
