2013/7/19 <[email protected]>: > Thank you for this. > I recalculated my distributions and make them a value between 0 and 1 at > large distances. If I submit then my own potential pot.in which goes to a > positive value in this case would votca not shift the potential after each > iteration to zero? Please, let me know. VOTCA always shifts the potential, to U(r_max)=0 for non-bonded interaction and U_min=0 for bonded interactions. This is why I said making VOTCA believe your interaction is bonded, might help. The update rule is the same for bonded and non-bonded.
Anyhow the shift doesn't change the physics, so why are you so bother about it? You could just to do IBI and shift the finial outcome once it is converged. Christoph > > Steven > > W dniu środa, 17 lipca 2013 17:43:51 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 2013/7/17 <[email protected]>: >> > Thank you for this. >> > >> > Another question - presumably I will specify my own distributions (not >> > from >> > VOTCA) with some simplifications. Then I will create intial potentials >> > to >> > IBI as name.pot.in. Votca will try to fit to my distributions to the one >> > submitted in the main directory. However, by calculating distributions >> > after >> > each step these will not be distributions which could possibly match my >> > initial with simpifications, am I right? Do I have to calculate RDFs at >> > each >> > step on my own then? >> 1.) If you give VOTCA a pot.in, it will not do use the potential of >> mean as initial guess in step_000, but just your potential. >> 2.) Independently of pot.in, VOTCA will always compare dist.new >> against dist.tgt every step >> 3.) dist.new is calculated in every iteration using csg_stat, you >> could make VOTCA fit only the part 0 to min. >> 3b.) You could write a custom post-update script to do whatever rdf >> calculation/ potential modification after you want. This can be used >> to overwrite rdf calculated by csg_stat. >> 3c.) All of this seems a bit hacky, why don't you just declare some >> interaction of type bonded, so csg_stat will calculate >> p(r)=H(r)/(4pi*r^2) instead of the rdf for those. >> >> > Another issue: How Votca normalize RDFs using csg_stat ? I wish to have >> > volume and mass normalized distributions, is that possible? >> No, we don't have an option to calculate the volume and mass >> normalized distributions instead. Though it is not hard to implement! >> For IBI that would also make no difference as all normalization >> factors drop out in the ratio g(r)/g_target(r) used in the update. >> >> Christoph >> >> >> > >> > Steven >> > >> > W dniu wtorek, 16 lipca 2013 23:17:05 UTC+1 użytkownik Christoph >> > Junghans >> > napisał: >> >> >> >> 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. >> > >> > >> >> >> >> -- >> 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. 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