Thanks Christoph, Indeed the csg_stat and csg_boltzmann gives same distribution. I far as I understand VOTCA, this is always true. So, how does one take care this type of scenario where one has faint minima in the normalized plot. I can always take the un-normalized plot as the guess potential. Would this be the right approach?
Any insight would be very helpful. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Aug 30, 2013 at 10:08 AM, Chandan Choudhury <[email protected]>wrote: > > > On Thu, Aug 29, 2013 at 10:42 PM, Christoph Junghans > <[email protected]>wrote: > >> 2013/8/29 Chandan Choudhury <[email protected]>: >> > >> > On Thu, Aug 29, 2013 at 10:14 PM, Christoph Junghans < >> [email protected]> >> > wrote: >> >> >> >> 2013/8/29 Chandan Choudhury <[email protected]>: >> >> > Dear votca users, >> >> > >> >> > I have an angle distribution of beads, such that it peaks ~2.85 rad >> (163 >> >> > deg, xvg, file (ABC.angle) is attached). Now if I do Boltzmann >> inversion >> >> > on >> >> > it (with normalization 1/sin), it produces a very faint hump, >> actually >> >> > no >> >> > minima exists, around 2.8 rad (Fig ABC.angle.pot attached). In this >> >> > case, >> >> > how would the beads sample the region. Or how would votca take care. >> >> How did you arrive at ABC.angle.pot? Is ABC.angle already normalized >> with >> >> /1sin? >> >> If I plot log(ABC.angle) it has a minimum! >> >> >> > >> > ABC.angle.pot is the outcome of csg_boltzmann. It is not normalized with >> > 1/sin. Without the normalization it does has the minimum. >> Have you checked that you get the same with csg_stat? >> > > Yes. csg_stat and csg_boltzmann gives the overlapping distributions. > >> > >> >> >> >> > >> >> > Also, can someone help me to understand the origin of normalisation >> by >> >> > 1/r^2 >> >> > and 1/sin for bonds and angle, respectively. >> >> 1/sin and 1/r^2 are just volume elements, which are needed as bigger r >> >> (angles around pi/2) are more likely to happen due to volume variable >> >> space. >> > >> > Thanks for the explanation, >> >> >> >> >> >> Have a look at this paper and its supporting information for some >> >> examples of angle potentials: >> >> "Multiscale simulation of small peptides: Consistent conformational >> >> sampling in atomistic and coarse-grained models" >> >> Olga Bezkorovaynaya, Alexander Lukyanov, Kurt Kremer, Christine Peter >> > >> > >> > I will surely have a look at this. >> > >> > Thanks >> >> >> >> >> >> >> >> >> >> > >> >> > Thanks >> >> > >> >> > 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. >> > > -- 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.
