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!
> > 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. 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 > > 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.
