2013/9/13 Chandan Choudhury <[email protected]>: > > Dear Christoph, > > I am attaching the bonded distribution of BC bond and the corresponding > potentials. The distributions show the sudden increase and there is also a > discontinuity in the potentials, Can you suggest me how can this be avoided. This is not exactly a discontinuity, the slops is just slightly higher for smaller r. Also, have a look if the correspond table_b*.xvg is okay. I would also check the full distributions (copy your settings.xml, and change min to 0 and max to bigger number and run csg_stat manually in a iteration step.)
You could also increase r min to 0.355, as there is anyway not much information in the last bin. Christoph > > N.B: I have periodically changed the min and max for BC from 0.348 to 0.354 > for min and 0.398 to 0.392 for max. This BC is iterated every step while > others are not iterated. > > Chandan > > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Fri, Sep 13, 2013 at 10:00 PM, Chandan Choudhury <[email protected]> > wrote: >> >> >> >> On Fri, Sep 13, 2013 at 9:21 PM, Christoph Junghans <[email protected]> >> wrote: >>> >>> 2013/9/12 Chandan Choudhury <[email protected]>: >>> > Dear votca users, >>> > >>> > I am trying to iterate the bonded distributions using IBI in votca >>> > 1.3-dev. >>> > We need to specify the min and max for each of the bonded >>> > distributions. It >>> > seems to me that these cut-offs are very crucial, as the new >>> > distributions >>> > and the update to the potential are computed in this regime. >>> > Surprisingly, what I find that at the end of this region, some thing >>> > messy >>> > is happening for the new distributions. There is an abrupt increase in >>> > the >>> > distribution. I will clarify the observations with the specific plots >>> > (attached). >>> > >>> > AB.bond.dist.tgt is the target distribution for the AB.bond. >>> > AB.bond.dist.new is the distribution generated in the 5th iterative >>> > step. >>> > AB.bond.dist.new_0.0-0.6 is the distribution generated using the >>> > trajectory >>> > of the 5th step and modifying the min (0.0) and max (0.6) in the >>> > setting >>> > file. >>> > >>> > We see that there is an sudden rise in the distribution at the min side >>> > of >>> > AB.bond.dist.new. What I also feel that this discontinuity will affect >>> > the >>> > updated potential and also force. >>> > >>> > Can some one help me regarding this. Any guidance is appreciated. >>> How does your potential (pot.cur) in the 5th step looks like? >>> Especially check for small r for artificial behavior. >>> >> Thanks for the reply. >> >> pot.cur (attached) looks fine. That means the potentials are not affected >> by the discontinuity. So, how can this be avoided in the distributions. >> >> Chandan >>> >>> Christoph >>> > >>> > Chandan >>> > >>> > >>> > >>> > -- >>> > Chandan kumar Choudhury >>> > NCL, Pune >>> > INDIA >>> > >>> > -- >>> > 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 http://groups.google.com/group/votca. >>> > For more options, visit https://groups.google.com/groups/opt_out. >>> >>> >>> >>> -- >>> 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 http://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/groups/opt_out. >> >> > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
