You mentioned "First, have a look at your ACI-ACI.dist.tgt again, this distribution doesn't go to one* hence the potential doesn't go to 0 for large r*. "
RDF goes to 0 due to the fact that the system is heterogenous. However, my potentials goes to 0 which is correct. Steven W dniu poniedziałek, 15 lipca 2013 21:27:20 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/15 <[email protected] <javascript:>>: > > > > > > W dniu poniedziałek, 15 lipca 2013 21:09:27 UTC+1 użytkownik > > [email protected] napisał: > >> > >> Thank you for this. For heterogenous system RDF does not go to 1 but to > 0. > >> In this case I guess I need thousands of iterations... The system input > are > >> 15 potentials which makes it so complicated. > >> > >> Steven > > > > > > And to be clear: My potentials goes o zero at large r. > What do you mean? > > > > > Steven > > > >> > >> > >> W dniu poniedziałek, 15 lipca 2013 17:44:46 UTC+1 użytkownik Christoph > >> Junghans napisał: > >>> > >>> 2013/7/15 <[email protected]>: > >>> > Votca is definitely wrong. If you take the example of maximum of my > >>> > ACI-ACI.dist.tgt the maximum corresponds to 65.555. The potential at > >>> > this > >>> > point should be: W = -2.49435*ln(65.55) = -10.433 and in my > >>> > ACI-ACI.dist.pot > >>> > the value corresponds to -16.1 - it is a huge difference and that is > >>> > why my > >>> > further distributions are so huge.... > >>> No, Votca is 100% correct, and does what it is supposed to do. > >>> > >>> First, have a look at your ACI-ACI.dist.tgt again, this distribution > >>> doesn't go to one hence the potential doesn't go to 0 for large r. > >>> And that is mainly the reason why VOTCA cannot handle it, > >>> ACI-ACI.dist.tgt is not a common rdf! > >>> You will have to provide an initial guess (pot.in) to make it work. > >>> (Please also read my email from July 10th again.) > >>> > >>> Second, VOTCA does exactly what it is supposed to do. Go into gnuplot > and > >>> run: > >>> p [0:3][-20:5] "ACI-ACI.dist.tgt" u 1:(-2.49435*log($2)-5.7) w l, > >>> "ACI-ACI.pot.cur" w l > >>> Except for some small deviations, which come from the cubic spline > >>> interpolation, there is no difference in the curves. > >>> As Victor said before, VOTCA shifts the potential to be zero at the > >>> cutoff -> -10.433 - 5.7 = -16.1. This shift of 5.7 makes no difference > >>> for the thermodynamics however. > >>> > >>> Third, even pot.new is correct. Run > >>> $ paste ACI-ACI.dist.new <(sed '/^#/d' ACI-ACI.dist.tgt) <(sed '/^#/d' > >>> ACI-ACI.pot.cur) > ACI-ACI.temp > >>> to generate a temp file. > >>> And go into gnuplot and plot: > >>> p [0:3][-20:5] "ACI-ACI.temp" u 1:(2.49435*log($2/$5)+$8-16.1) w l, > >>> "ACI-ACI.pot.new" w l > >>> There is basically no difference in the curves. > >>> > >>> Conclusion: > >>> - check your distributions again > >>> - provide pot.in for the interaction, which don't have a "common" rdf > >>> (meaning which doesn't go to 1) > >>> > >>> Christoph > >>> > >>> > >>> > > >>> > > >>> > > >>> > > >>> > W dniu poniedziałek, 15 lipca 2013 12:59:40 UTC+1 użytkownik > >>> > [email protected] napisał: > >>> >> > >>> >> > >>> >> > >>> >> W dniu poniedziałek, 15 lipca 2013 12:42:37 UTC+1 użytkownik Victor > >>> >> Rühle > >>> >> napisał: > >>> >>> > >>> >>> Dear Steven, > >>> >>> > >>> >>> provided the same kBT was used, I can think of two issues which > might > >>> >>> lead to these differences > >>> >>> > >>> >>> 1) votca can shift the potential, but the shape should match. That > >>> >>> can in > >>> >>> particular happen if you cut the rdf in a region where there are > >>> >>> still > >>> >>> modulations. > >>> >>> 2) What type of potential are you lookin at? For bonds and angles, > >>> >>> there > >>> >>> is indeed a normalization necessary, see > >>> >>> > >>> >>> > >>> >>> http://dx.doi.org/10.1002/(SICI)1521-4044(199802)49:2/3 > <61::AID-APOL61>3.0.CO;2-V > >>> >> > >>> >> > >>> >> Thank you. I am looking at the nonbonded interactions only. The > shape > >>> >> of > >>> >> the potential matches but the minima is lower than from my > calulation. > >>> >> There > >>> >> is no normalization for non bonded so this is weird. I cut it at > the > >>> >> begining as there were very small values and Votca was not able to > >>> >> extrapolate it properly. > >>> >> > >>> >>> > >>> >>> > >>> >>> Your second point indeed sounds a bit weired. Could you please > post > >>> >>> these > >>> >>> few curves to help debugging (i.e. the <name>.pot.cur, > <name>.pot.new > >>> >>> <name>.dist.tgt <name>.dist.new of the iteration 1 folder)? > >>> >>> > >>> >>> Victor > >>> >> > >>> >> > >>> >> Please, see attached. > >>> >> > >>> >> > >>> >>> > >>> >>> > >>> >>> > >>> >>> 2013/7/15 <[email protected]> > >>> >>>> > >>> >>>> Dear Votca Users, > >>> >>>> > >>> >>>> I have to issues with IBI: > >>> >>>> > >>> >>>> 1) I took one my ditributions and calculated on my own potential > W= > >>> >>>> -kBT > >>> >>>> ln(RDF) and I got different potential than Votca provide me. For > >>> >>>> instance > >>> >>>> lets calculate the potential minimum for the distribution maximum > of > >>> >>>> 162. > >>> >>>> Pot = -.249435*ln(164) = -12.69. The minimum of Votca potential > >>> >>>> corresponds > >>> >>>> to approximately -16 kJ/mol. Where I missed something? is it > somehow > >>> >>>> normalized? > >>> >>>> > >>> >>>> 2) After 1st iteration my distribution was much higher than the > >>> >>>> target > >>> >>>> one so I guess the potential should decrease but apparently the > new > >>> >>>> potential has deeper minima so the next distribution has a even > >>> >>>> higer > >>> >>>> distribution. Could anyone please explain me this? > >>> >>>> > >>> >>>> Steven > >>> >>>> > >>> >>>> > >>> >>>> -- > >>> >>>> 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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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