I am kinda confused here. Lets say I have mixture of two molecules, one with more than one atoms and second one is just simple one atom molecule, call it as CG1.
Then I wish to coarse-grain multi-atom molecule to its COM site, call it as CG2 and now determine what is the effective CG potentials between CG2-CG2, CG1-CG2, I dont have to worry about CG1-CG1 which I know already. The trajectory contains the force information due to all possible interactions. So to determine CG2-CG2, do I have to eliminate any interaction between CG2-CG1, and same for CG1-CG2 i.e. eliminate CG2-CG2,CG1-CG1. Or FM takes of these by itself. That is to say when computing CG2-CG2 it only considers force acting on CG2 site only because of CG2-CG2 interaction and not any other. Yeah, it would be great if you could forward me the paper you submitted in regard to this topic. thanks sikandar On Thu, Mar 10, 2011 at 5:34 PM, Victor Ruehle <[email protected]> wrote: > Hey, > > how do you want do describe interactions between coarse-grained and > atomistic molecules? Each atom with coarse-grained site? How many > different atom types and with that interactions will you have then? > Also be aware that mixing resolutions might lead to additional > problems. > > Currently the only way to keep one molecule at atomistic resolution in > force matching is by specifying a 1:1 mapping files, which maps each > atom to one coarse-grained bead. However, what you plan to do is not > trivial since your trajectory has the full forces, also the ones which > you don't want to parametrize. If you can do a clean splitting, either > by excluding interactions, or by subtracting already known ones (this > feature was added in 1.1) this might work. We recently submitted a > paper on this, I can send you the draft if you want. > > Victor > > 2011/3/10 Sikandar Mashayak <[email protected]>: > > Hi > > I want to perform a Force Matching on a reference system which contains > two > > types of molecules. I am planning to CG one of it and keep the other in > > all-atom description. > > So I am wondering how do I specify options in fmatch.xml file? Will I > have > > to specify non-bonded interactions for CG-CG and each pair of CG-atoms of > > other molecule? > > thanks > > sikandar > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
