2013/7/24 <[email protected]>: > I am also trying to iteratively get distribution for 1 of my interactions > leaving other 14 being fully repulsive.... My potential at step 124 has a > much deeper minima than the initial one... And ditribution is much higher > than the target one obviously... These beads of which potential i am trying > to get stay in a globular conformation...There must be something wrong.. > Please, see attached my files, any help appreciated. Like I said before the absolute value of the deepness doesn't matter! What matter is the shape around the min + 3k_BT. You can shift your potential by 1mio kJ/mol the thermodynamics will still be the same.
> > Steven > > > > W dniu wtorek, 23 lipca 2013 20:05:45 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 2013/7/23 <[email protected]>: >> > >> > >> > W dniu wtorek, 23 lipca 2013 16:24:25 UTC+1 użytkownik Christoph >> > Junghans >> > napisał: >> >> >> >> 2013/7/23 <[email protected]>: >> >> > Another example which seems to be correct but wish to know, please >> >> > see >> >> > attached. The derivative (last column) of function H(x) is zero while >> >> > H(x) >> >> > is highly positive... Is that correct potential? >> >> I don't see a problem here, the begin of the potential is constant and >> >> hence the derivative is zero. >> >> >> >> > My protein still stays in a >> >> > globular conformation and I corrected other potentials. If it is ok >> >> > would >> >> > you try to make IBI with potentials one by one? >> >> do_potential in the xml file allows you to divide interactions into >> >> group to update only one group at the time. >> >> The default will put all interactions in one group. >> >> >> >> I would approximate your 4 special interactions by a non-linear >> >> spring-like potential (see my earlier email) and keep them fixed for >> >> now and do IBI on the other 11 interactions. >> > >> > >> > The problem is that all 15 of my distributions goes to zero as there is >> > nothing at large distances. I already have angles take from atomistic >> > simulations, by one boltzmann inversion I got great results (tabulated >> > angles). Now I shifted my distributions to RDF = 1 which option 1. Then >> > I >> > should use: >> > for the 1st potential >> > potentia.update 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >> > for the second >> > potential.update 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 >> > etc. am I right? >> Yes! >> >> > >> > The other option would be to to use the non-linear spring as for bonded >> > (you >> > mentioned before). Does only Votca 1.3 supports it? Is there any >> > tutorial? >> > Which option would you recommend? >> I meant to Boltzmann invert the distribution and use it as >> table_bX.xvg and keep it fixed. >> But it will depend on your system if this approach will work or not. >> >> >> > >> > Steven >> > >> > >> >> >> >> >> >> >> >> > >> >> > Steven >> >> > >> >> > W dniu wtorek, 23 lipca 2013 10:22:26 UTC+1 użytkownik >> >> > [email protected] >> >> > napisał: >> >> >> >> >> >> Could you please also explain me why from attached potential Votca >> >> >> produce >> >> >> a table with negative (close to zero) values at low distances? It >> >> >> does >> >> >> not >> >> >> make sense and hence my protein remains globular... I have 4 >> >> >> potentials >> >> >> like >> >> >> this out of 15... >> >> >> >> >> >> Steven >> >> >> >> >> >> W dniu poniedziałek, 22 lipca 2013 23:40:50 UTC+1 użytkownik >> >> >> Christoph >> >> >> Junghans napisał: >> >> >>> >> >> >>> 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. >> >> > 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.
