On Thu, Apr 19, 2018 at 8:44 AM, Alexander Alexander <[email protected]> wrote: > Hi Christoph, > > On Thursday, April 19, 2018 at 12:19:49 AM UTC-4, Christoph Junghans wrote: >> >> On Wed, Apr 18, 2018 at 9:39 PM, Alexander Alexander >> <[email protected]> wrote: >> > Hi >> > Any ideas please? >> Sorry, there was no question in your previous email, so I thought it >> was just FYI. >> >> Honestly I haven't seen that kind of issue before. >> Try to set the min of LG-L, LG-LG and LG-H1 a bit higher, e.g. 0.25 or 0.3 > > Increasing the min can not help, as I tested for another system. > > You know, the system has 4 beads LG (G)-H1(H)-L(L)-RG(G) ,inside parenthesis > are the bead types. And the exclusion defined in cg-mapp.xml is as > following: > <name>exclusion</name> > <beads> > LG RG > </beads> > </bond> > And issue happens wherever LG is involved as I explained earlier. > > In a new system which has 5 beads as LG (G)-H1(H)-H2(H)-L(L)-RG(G), for > which the exclusion defined in cg-mapp.xml is as following: > <name>exclusion</name> > <beads> > LG L > H1 RG > </beads> > </bond> > Now, in the new system, addition to the LG, the problem also happen wherever > H1 is involved. > The point is that in both systems, the problem shows up for the beads types > with more than one bead repetition. Like bead type G with LG and RG beads in > the first system. And types G (beads LG and RG) and H (beads H1 and H2) in > the second system. > Don't you think somehow the portion of the repetitive bead is missing in > calculations? I am not sure what you mean, but you can always cross-check the distribution calculation with gmx rdf.
> > Another question: altering min/max ... in the settings.xml during simulation > (for instance between step_n and step_n+1) causes crashing the job, so how > to change them without starting a simulation from scratch? I think you should be able to just remove the last (incomplete) step. Otherwise, you just can use pot.new from the last step as a pot.in for a new simulation from scratch. Christoph > Thank you. > Regards, > Alex >> >> >> Christoph >> >> > >> > Regards, >> > Alex >> > >> > -- >> > 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. -- 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.
