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/CAHG27e491r%2BoML9dv3P5qtCBMaeQvo7c7%3DMuO2T%2BET%3DHwTb-9A%40mail.gmail.com.
