Do you mean that instead of iterating bonded and non-bonded interactions together, I just obtain the bonded ones in the beginning from a simulation of a single-chain in vacuum?
And instead of generating an exclusions list and later including it in the topology, I use number of exclusions as 2 in the topology of the coarse-grained system so as to exclude beads that are connected by bonds and angles. I presume both serve the same purpose? -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.
