Thanks Christoph! I'll try that script out. Another question: Right now my system consists of just a single chain of polyacrylamide in water. My polymer consists of 2 types of beads, A and B. Now, to capture the non-bonded interaction between the beads, I get the following rdfs A-A, B-B, A-B, taking care to exclude 1-2 and 1-3 interactions. All three rdfs converge to zero because it is just a single chain in a large box of water. Would IBI do the convergence of such rdfs? Or should I obtain polymer-polymer rdf from a melt system?
Thanks! -Pallavi Banerjee On Monday, October 19, 2015 at 11:21:13 AM UTC+5:30, Pallavi Banerjee wrote: > > Hello all, > > My system is polyacrylamide in water. I need to coarse-grain the system > traversing through a concentration range. What I plan to do is IBI using > the MARTINI water model since this water model gives a viscosity value > close to that of SPC-E (water model in my atomistic system) and viscosity > is the major property of interest in my case. IBI would then be carried out > to optimize the potentials between the polymers and polymer-water, whereas > the water-water interaction would be directly taken up from MARTINI. Since > MARTINI uses a 4:1 mapping, I was wondering whether this idea would be > viable if I am to use votca. > > Thanks in advance! > > -Pallavi Banerjee > -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
