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.
