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. > > > > 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.
