2013/7/15 <[email protected]>: > 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 > > 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]. > 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.
