Thanks for the replies! Yes, I want to coarse-grain a dilute benzene in bulk water - 2 monomers, with a half-open harmonic wall at 12 Angstrom (so no effect at short range, but preventing the centers of mass of the benzene to drift apart further than that). Each benzene molecule is described by three sites (to capture the orientation of the benzene plane), and I would like to obtain a pairwise potential between sites (as all sites are of the same type, there's just a single potential). I've managed to sort out my RDF and the initial potentials, and I can run the code, but the potential updates don't make any sense (see attachment) - which I guess is due to what you said, that IBI is not applicable to dilute systems? Thanks for pointing that out to me, I hadn't been aware of this limitation. Is there another similar/related method that generates pairwise site-site potentials based on the site-site distance distribution from my all-atom simulations? (The (half-open) harmonic restraint shouldn't come into it, as its only purpose is to increase the 'interaction rate' of the dimer by preventing them to drift apart indefinitely once they break out of their bonded state.)
best, ST On Wednesday, April 6, 2016 at 7:01:36 AM UTC+1, Denis Andrienko wrote: > > Hi, > > I am not sure what exactly you are doing but it looks like you are > trying to find a coarse-grained interaction potential for a dilute > system (benzene in water). If this is the case, IBI is not the method to > use. You can calculate the average force on your harmonic restraint as a > function of r (restrain distance), integrate over r and subtract the > entropic part (1/r scaling). You will then get your potential of mean > force. If you have three equivalent beads, divide it by 3. You > might need to do umbrella sampling to get good statistics for short > separations. > > Best, > Denis > > -- 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.
ibi_benzdimer.pdf
Description: Adobe PDF document
