Hi, I'd like to coarse-grain a benzene dimer - originally solvated in a periodic box of water (L=29.547 Angstrom), and I want to obtain a solvent-free CG description (three sites per benzene molecule), generating a non-bonded pair potential between the sites using IBI.
To keep the dimer from drifting apart, I've added a harmonic restraint (between centers of mass of the monomers) starting at 12 Angstrom, already in the full atomistic simulations. I'm using LAMMPS for the MD, and to keep things comparable I'd like to have the harmonic restraint explicitly as a spring/couple fix in the MD, rather than implicitly in the non-bonded potential. The harmonic restraint would show up in the Boltzmann inversion first guess at the non-bonded potential, so I thought of using a force-matching-based potential as an initial guess. Has anyone used VOTCA/CSG for such a case before? I could only find monomers in vacuum, no mention of dimers in vacuum or a large box. So on the one hand I tried describing the system as a single 'molecule' with different types of sites for each monomer, so that the non-bonded distances are seen as 'bonds' - in this case I can get the same distribution function from csg_stat and my own routine, but the potential updates seem to go wrong. On the other hand I looked at the system as two molecules with one type of site, but I think I am stuck there because I don't know how csg_stat produces the rdf in this case, so probably my way of generating the target distribution doesn't match and hence the IBI procedure can't get anywhere. How should I calculate the 'RDF' in this case? Given that it goes to zero at large distance (due to the restraint), not to one. Any help appreciated - please let me know if I should provide more details! Thanks, ST -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
