2015-10-20 12:19 GMT-06:00 Pallavi Banerjee <[email protected]>: > 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? Yes, do the bonded interaction from a single chain in vacuum using simple Boltzmann inversion and the non-bonded for e.g a melt simulation using iterative Boltzmann inversion. But I would really recommend you read 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) and the references therein especially
W Tschöp, K Kremer, J Batoulis, T Burger, and O Hahn. Simulation of polymer melts. i. coarse-graining procedure for polycarbonates. Acta Polymerica, 49:61–74, 1998. > > 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? nexcl is not exactly the same as an exclusions list. In a single chain in vacuum simulation you want to exclude all interaction, which are later covered by non-bonded interactions. (see section 2.2.1 for the details) Christoph > > > -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.
