Got it, thank you Christoph. On Monday, August 30, 2021 at 6:19:25 PM UTC-4 Christoph Junghans wrote:
> 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/aa344d8c-af46-44cf-bd29-4d1071013108n%40googlegroups.com.
