2013/9/3 Chandan Choudhury <[email protected]>: > 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? I not sure here, I leave this question to the bio-guys on this list.
> > 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. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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