Pragati, you could use http://stock.cmm.ki.si/smt/, but for that size of a system you might need to write a little python script yourself.
Christoph On Wed, Feb 24, 2021 at 3:36 AM Pragati Sharma <[email protected]> wrote: > > Dear all, > > I am trying to perform IBI for a 500-mer polymer chain (Each monomer has 4 > carbons and 6 Hs) > > I have tabulated potentials from IBI for a 10-mer and 32-mer chain > containing 320 atoms and I will use these potentials to simulate the 500-mer > polymer. > > However, a 500-mer polymer contains 5002 atoms. I need conf.gro and topol.top > to run the simulation. And for that I need to map the atomistic structure > files. Making a mapp.xml file for 5002 atoms (Each bead is made of 3 carbon > atoms and 4-5 Hs) and giving individual bonds and angles would be a tedious > task. > > > Is there a way, other than using a mapp file to produce conf.gro for coarse > grained simulations. I have atomistic 500-mer chain simulations and > 10mer-32mer CG simulation files. > > Thanks for any idea on this. > > -- > 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/CAMpF9Q1MAJ1AfUrCCB%2BOv1UAqXNH9z1yAsC%3DC8QuZaEUmqdYig%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/CAHG27e5fMSTxy7bWf-My4C1-htb_SyjXBx_N63PXXPwV0L-2fA%40mail.gmail.com.
