Dear Christoph, After several trials with the suggestions from you and Vitalie, I still cannot obtain the nonbonded interactions. So I switch to the explicit solvent model, then I get the converged interactions, although I don't want to use the explicit model, but it seems to be the only way I can do currently. Thank you and Vitalie for all the help! Best regards, Zidan
On Tuesday, 20 September 2016 19:13:49 UTC+2, Christoph Junghans wrote: > > 2016-09-20 2:11 GMT-06:00 Zidan Zhang <zhang...@gmail.com <javascript:>>: > > 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+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com > <javascript:>. > > 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.
