On Sun, May 28, 2023 at 11:56 PM Kankana Bhattacharjee <[email protected]> wrote: > > Dear Sir, > > I am practicing the votca tutorial for propane molecule. I am trying to > generate .itp file of CG propane. For that I used the command line: > csg_gmxtopol --topol.tpr --cg propane.xml --out cg.top, then obtained the top > file. But, there bond length and angle value between the beads is not > mentioned. How to get those bonded information of the beads so that, I can > run GROMACS simulation of the CG system ?
csg_gmxtopol only generates a template that can be used as a starting point. In most cases you will have to edit it. The bond and angle length you will have to estimate from the distributions. > > Also, I have gone through the topol.top file of the system using "ibi", "imc" > methods. But, there I dint understand how to use the function type for the > bonds, angles and how non-bonded settings is decided ? In most cases people use tabulated interaction for everything. Have a look at: https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/topol.top#L23 type =8 is tabulated. 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/d54cdf42-089b-455e-892e-ce99327c7184n%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/CAHG27e5-dAy3JmbR3maaxqb23DuC%2BunO6YCdEzUW1EE_HERs_w%40mail.gmail.com.
