That sounds like what I was hinting at: from what I understand, you're simulating a single protein, not a pure liquid of stuff. So your RDF will never go to 1 because there won't be anything at large distances. Is that the case? If so, more iterations and/or better initial guesses won't cut it.
On Mon, Jul 15, 2013 at 10:09 PM, <[email protected]> wrote: > 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 > > 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. > > -- You received this message because you are subscribed to the Google Groups "votca" group. 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