2013/7/16 <[email protected]>: > > > W dniu wtorek, 16 lipca 2013 08:48:51 UTC+1 użytkownik Tristan Bereau > napisał: >> >> 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. > > > Yes, this is the case. I will aproximate the RDFs so that they go to sth > which is non zero. Thank you. non zero will not be enough, it has to be 1 otherwise your potential will still accumulated whatever the value, kT*log(P(r_cut), at the cutoff is.
For me the distributions looks more like a something, which could be modeled with a non-linear spring type potential (r-> +/-inf P->inf), where the minimum is a zero. VOTCA could do that for you if declare the interaction as bonded. (VOTCA's definition of non-bonded and bonded might not be taken too strict.) Also from the modeling point of view, it might make sense to have a spring between some beads, which cannot go infinitely apart due to geometry. Anyhow, these are scientific decisions you have to make yourself. Christoph > > Steven >> >> >> 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. > 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.
