Hi all, i'm having problems with my iBI simulation results, the distribution function is not converging after 150 iterations:
i'm trying to run coase-graining simulations of polyethylene using IBI method. The atomistic system consisted on 10 chain molecules with 50 DP simulated with LAMMPS using the COMPASS forcefield from where i dumped the RDF, bond, and angle distributions. Either RDF and bond distribution obtained from atomistic simulation where similar in shape with the ones obtained for hexane in "Macromol. Theory Simul. 20, pp 472-477 (2011)". For the IBI simulation i want to map 5 monomers into a coarse-grained particle resulting on a system with 10 chains with 10 beads per chain. I generated all the files required for the IBI simulation, including exclusions file, using Votca tools. Angle and bond interactions (table_a1.xvg and table_b1.xvg) where obtained by Boltzmann inverting the distribution functions and then using "csg_call convert_potential xvg" script. For non-bonded potential i let Votca to do the inversion after calling "csg_inverse". I'm assuming that all the particles are of the same type, which means that terminal and inner chain particles are equal and the terminal hydrogens on the methylenes are neglected. In the grompp file i set a time-step of 1 ps and a simulation time of 1ns using stochastic dynamics integrator at 450K. The cutoff where set to 1.5 nm. At this moment i'm not using any kind of pressure correction and after each iteration the distribution function is smoothed twice. With this setup, after running IBI the results don't converge, the distribution function that i'm obtaining at the end of each iteration show strange shapes and the convergence values are always in the range of 0.36 - 7. Other thing that concerns me is on how i should extrapolate to the right the bonded potential. The atosmistic results gives me a bonded distribution that goes to r=0.29 nm, the bond length of the coarse- grained system is much higher than this, so i need to extrapolate the bonded potential to higher values of r. I'm using quadratic function to extrapolate the table, but i'm not quite sure in which extent these extrapolated values are feasible. I wonder if someone can help me. Is anything wrong with my setup??? Is there something missing that i should account with?? Thanks a lot in advance, Sacha -- 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.
