Thank you sir. I would like to know, how can one get gromacs compatible itp file for a Coarse grained model using votca ?
[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 > -- 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/CAMNJFVnGX%3D0uRTvTC1X7nrb8PujqxcfDr6b6SP6xLCAymuQh0A%40mail.gmail.com.
