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.
