2015-10-19 21:15 GMT-06:00 Pallavi Banerjee <[email protected]>: > 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? >From a single chain vacuum, one usually derives the intra-molecular interaction (e.g. bonds and angle). For the inter-molecular interaction one needs rdf from a melt simulation or a simulation in solvent.
See section 2.2.1 of the manual (https://github.com/votca/csg-manual/releases/download/v1.3_rc1/votca-csg-manual-1.3_rc1.pdf) Christoph > > 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. -- Christoph Junghans Web: http://www.compphys.de -- 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.
