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? > >> >> > >> > 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.
