2016-04-05 7:25 GMT-06:00 'ST' via votca <[email protected]>: > 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. I think, you could simply subtract the harmonic contribution from the Boltzmann inverted initial guess and use that one.
> > 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! I don't see why csg_stat would work for your case, it support open boundary conditions. You could also try to exclude the intra-molecular contributions to rdf. Christoph > > 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. -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
