On Mon, Aug 30, 2021 at 4:11 PM Satyen Dhamankar <[email protected]> wrote: > > I am looking at the hexane_cg.xml file in the tutorials, and I see that > bead A1, B, and A2 have the same mapping called UNITY, and the weights > assigned to that mapping is simply 1. > > I dont understand how this works. In the simple hexane.xml file, I have to > write down every single atom that corresponds to that bead, make sure I am > assigning the right weight to each atom, and give it a particular name. My > question is, why, when performing the CG potential optimization, it is the > same mapping, and the weight is given as 1? For example, since beads A and B > have different masses, I would expect you to have different maps, like you > have in the original hexane.xml file.
When you do a run with csg_inverse the topology is already a coarse-grained one, hence the mapping file is only needed to define the bonds/angles and so it is only a simple 1:1 mapping. In contrast, the hexane.xml is a mapping file from an automatic topology to a coarse-grained one. > > If I had a molecule which I have CG'd to beads A, B, C, D. For my > molecule_cg.xml file for ibi, will I do the same thing as you have done in > this example? Where the mappings have the same name? Basically, you will need to write a simple 1:1 mapping file with the beds A, B, C & D, apply the UNITY mapping everywhere and just add the cg_bonded section. Christoph > > I would appreciate any advice you have for me! > > -- > 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/a516c24a-6682-4a57-a11a-36e32cc7d3aen%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/CAHG27e6Xkzw2OeQLzki43qBN%2BJYg01vAjd9QH9QkD4wZn9FHWA%40mail.gmail.com.
