Some of the rdfs go very abruptly to 1, so you might want to try: - increasing the cutoff - using a bigger system - doing a PBC correction as in http://dx.doi.org/10.1063/1.4742067
Another option is to - add extra exclusion - use a fudge factor for the 1-4 interactions - adding a couple of special 1-4 interactions for that I would split the rdfs in inter-molecular and intra-molecular pairs and check if the parts agree to the atomistic case separately. Christoph 2016-09-18 3:10 GMT-06:00 Zidan Zhang <zhangzi...@gmail.com>: > The possible reason of mistaken the exclusions can be ignored, I have > already checked! > > > On Sunday, 18 September 2016 11:07:09 UTC+2, Zidan Zhang wrote: >> >> Dear All, >> As shown in enclosed material, I prepared a monomer system and a >> coresponding decamer system. For the coarse-grained level, I made the >> solvent implicit, and using three-beads mapping scheme for each structural >> unit. The IBI for monomer system and for bonded interactions of decamer >> system works well, but for the nonbonded interactions of decamer, all >> interactions have deviations from their atomistic targets. >> I have tried: >> 1. using different initial CG configuration; >> 2. change the temperature to modify the initial guess of the potential; >> 3. scale factor during the iteration; >> 4. a five-beads mapping scheme. >> All of these couldn't solve the problem, for some cases listed above, the >> decamers in the box get phase separation. >> Any suggestions? Thank you very much! >> >> Best regards, >> Zidan >> >> >> >> > -- > 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 votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
