Dear Marcc-André, are you now just asking about the technical aspect, or about the method itself? If the latter, there is no clear answer to your problem. There are various methods available. The first question you should ask yourself is what kind of properties you want to reproduce in with your coarse-grained model.
Most methods implemented in VOTCA are structure based approaches (or closely related to it) and therefore will most probably do wrong on thermodynamics. You can e.g. check the VOTCA references (http://www.votca.org/citations), there are also lot's of references given in the papers for more details on the method or links to other methods. That's still an incomplete list, but might be a good point to start with. If you want to act on the rdfs, I would start with IBI (see section in the manual). Otherwise, also force-matching or a hybrid approach might be worth a try. It's not yet officially supported in VOTCA, but depending on your system, it might be worth to have a look at what the MARTINI force field people did. Don't hesitate to ask any further questions, but providing some more details might help... Best, Victor 2011/9/1 Marc-André Dubois <[email protected]>: > Hi all, > I tried to follow the tutorials that you provide on your website. > Coarse-grained models are not actually the biggest concern of my group, so I > have to start from the basis. As I actually understand the thing, I have to: > > 1. constructs an atomistic representation of the system, which will give to > you data to construct the coarse grained representation. > 2. runs a molecular dynamic at the atomistic scale > 3. obtains the radial distribution function for each of your CG beads > > From step 1 to step 3, I think that everything works fine. From these steps, > how it is possible to find the actual interaction potentials of the CG beads > to constructs a forcefield that GROMACS will understand? I am sorry that this > question would seems trivial, but as I previously said, I am not familiar > with these kind of experiments. Thank you, > > Marc-André Dubois > > -- > 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.
