2013/7/22 <[email protected]>: > > > On Friday, July 19, 2013 8:02:01 PM UTC+1, Christoph Junghans wrote: >> >> 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 > > > Thank you. This what I will do - shift the final potential. what would be > the best cut off for IBI - is that the place where distributions have > maxima? That is a tricky question, to be honest I don't know. You might have to play with the cutoff a bit.
> > > Steven > > >> >> > >> > 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. > 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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