2016-09-20 2:11 GMT-06:00 Zidan Zhang <zhangzi...@gmail.com>: > Dear Christoph, > Thank you so much for your advices. > - I have increased the cutoff to 3.0 nm, this time all the rdfs go steadily > to 1, but no obvious improvement can be observed within 52 steps, the plots > in the attachment have the lowest convergence (at 41 step); > - the current system contains 100 decamers (each chain contains 10 > structural units), the box length is 10 nm, and with 6500 solvent molecules > (not water, 2-Butanone), 40 ns NVT simulation, is it big enough? all types > of distributions look smoothly. If the *target* rdf haven't change for a bigger system, you are fine.
Christoph > > I will try the rest options. > > Thank you again! > Best regards, > Zidan > > > > On Monday, 19 September 2016 18:15:06 UTC+2, Christoph Junghans wrote: >> >> 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 <zhang...@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+un...@googlegroups.com. >> > To post to this group, send email to vo...@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. -- 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.
