On Tuesday, July 16, 2013 12:14:41 AM UTC+1, Christoph Junghans wrote: > > 2013/7/15 <[email protected] <javascript:>>: > > 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. > I meant, which potential you are referring to? > > The potential of main force U=- k_B*Tlog(g(r)), which VOTCA uses as an > initial guess, doesn't got to 0, it goes to infinity: > U(g(r)->0)=-log(g(r)->0) -> inf >
ACI-ACI.pot.new ACI-ACI.pot.cur - Yes, you are right. But I cut my potentials at zero and extrapolate it. Then once provided to Votca the distributions still increase. Shall I provide a "fake" distribution so it goes to 1 so then Votca will be converging y distributions with the potential cut at zero? > > > > > Steven > > > > W dniu poniedziałek, 15 lipca 2013 21:27:20 UTC+1 użytkownik Christoph > > Junghans napisał: > >> > >> 2013/7/15 <[email protected]>: > >> > > >> > > >> > 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]. > >> > 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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