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 ?
[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 > . > -- 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/CAMNJFVmG6oo0SjKt8%3Dj3RX%3DZVdxoYhvbwKyqB%2BaSMHT9q1Hqbw%40mail.gmail.com.
